Updated on 2024/11/03

Information

 

写真a

 
HIRAKAWA HIDEKI
 
Organization
Faculty of Agriculture Department of Bioscience and Biotechnology Professor
Graduate School of Systems Life Sciences Department of Systems Life Sciences(Concurrent)
School of Agriculture Department of Bioresource and Bioenvironment(Concurrent)
Graduate School of Bioresource and Bioenvironmental Sciences Department of Bioresource Sciences(Concurrent)
Graduate School of Bioresource and Bioenvironmental Sciences Department of Bioscience and Biotechnology(Concurrent)
Title
Professor

Papers

  • Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum)

    Nagasaki, H; Shirasawa, K; Hoshikawa, K; Isobe, S; Ezura, H; Aoki, K; Hirakawa, H

    DNA RESEARCH   31 ( 5 )   2024.10   ISSN:1340-2838 eISSN:1756-1663

  • Identification of Novel Red Pigment Biosynthesis Gene Locus in Quinoa Chromosome 1B

    Kushino Sayako, Nishimura Kazusa, Mizuno Nobuyuki, Ueno Mariko, Takeuchi Naoko, Nakano Ryohei, Iwahashi Yu, Kobayashi Yasufumi, Fujita Yasunari, Shirasawa Kenta, Hirakawa Hideki, Yasui Yasuo, Katsura Keisuke

    Abstracts of Meeting of the CSSJ   258 ( 0 )   18 - 18   2024.9

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    Language:Japanese   Publisher:CROP SCIENCE SOCIETY OF JAPAN  

    DOI: 10.14829/jcsproc.258.0_18

    CiNii Research

  • Genome information and its industrial applications for plants

    Hirakawa H., Hasegawa M., Yokotani N., Isobe S.

    Acta Horticulturae   3 ( 1404 )   5 - 18   2024.9   ISSN:05677572

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    Publisher:Acta Horticulturae  

    With current advances in sequencing technologies, genome sequences of various kinds of plant species have been determined at the chromosome scale. Accordingly, genome information, such as genome and gene sequences as well as gene functions, has accumulated. Currently, we have determined the genome sequences of more than 30 plant species by using next generation sequencing technologies. Besides, we have joined to the database project in 2nd period (2018-2022) of the Cross-Ministerial Strategic Innovation Promotion Program (SIP) aimed to apply the genome information to industrial fields. In the project, we have generated a data set Gene Curation DS to curate crucial information related to the following gene functions of plant species. 1) Functionally important genes described in the literature were curated according to their correspondence between the gene names appearing in the literature and gene IDs defined in genome sequences (112 species); 2) resistance gene analogs (RGAs), which are considered potential resistance genes (R-genes) against pathogens by producing R proteins, were searched for in genome sequences (134 species); 3) genes included in patent applications registered in the DNA Data Bank of Japan (DDBJ) were searched for in genome sequences (152 species); 4) gene functions were predicted by similarity searches against UniProtKB (the UniProt knowledgebase, which provides a comprehensive, high-quality, and freely accessible resource for protein sequences and functional information), Araport (a complete annotation of Arabidopsis thaliana), and EggNOG (a hierarchical, functionally and phylogenetically annotated orthology resource) (188 species); 5) orthologous groups of genes among 136 plant species were explored. Gene Curation DS has been released at http://fgi.kazusa.or.jp/gcds. We expect this data set to provide useful information for both fundamental research and industrial applications such as molecular breeding, including genome editing.

    DOI: 10.17660/ActaHortic.2024.1404.2

    Scopus

  • Chromosome-level genome assemblies for two quinoa inbred lines from northern and southern highlands of Altiplano where quinoa originated

    Kobayashi, Y; Hirakawa, H; Shirasawa, K; Nishimura, K; Fujii, K; Oros, R; Almanza, GR; Nagatoshi, Y; Yasui, Y; Fujita, Y

    FRONTIERS IN PLANT SCIENCE   15   1434388   2024.8   ISSN:1664-462X

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    Language:English   Publisher:Frontiers in Plant Science  

    Quinoa is emerging as a key seed crop for global food security due to its ability to grow in marginal environments and its excellent nutritional properties. Because quinoa is partially allogamous, we have developed quinoa inbred lines necessary for molecular genetic analysis. Our comprehensive genomic analysis showed that the quinoa inbred lines fall into three genetic subpopulations: northern highland, southern highland, and lowland. Lowland and highland quinoa are the same species, but have very different genotypes and phenotypes. Lowland quinoa has relatively small grains and a darker grain color, and is widely tested and grown around the world. In contrast, the white, large-grained highland quinoa is grown in the Andean highlands, including the region where quinoa originated, and is exported worldwide as high-quality quinoa. Recently, we have shown that viral vectors can be used to regulate endogenous genes in quinoa, paving the way for functional genomics to reveal the diversity of quinoa. However, although a high-quality assembly has recently been reported for a lowland quinoa line, genomic resources of the quality required for functional genomics are not available for highland quinoa lines. Here we present high-quality chromosome-level genome assemblies for two highland inbred quinoa lines, J075 representing the northern highland line and J100 representing the southern highland line, using PacBio HiFi sequencing and dpMIG-seq. In addition, we demonstrate the importance of verifying and correcting reference-based scaffold assembly with other approaches such as linkage maps. The assembled genome sizes of J075 and J100 are 1.29 and 1.32 Gb, with contigs N50 of 66.3 and 12.6 Mb, and scaffold N50 of 71.2 and 70.6 Mb, respectively, comprising 18 pseudochromosomes. The repetitive sequences of J075 and J100 represent 72.6% and 71.5% of the genome, the majority of which are long terminal repeats, representing 44.0% and 42.7% of the genome, respectively. The de novo assembled genomes of J075 and J100 were predicted to contain 65,303 and 64,945 protein-coding genes, respectively. The high quality genomes of these highland quinoa lines will facilitate quinoa functional genomics research on quinoa and contribute to the identification of key genes involved in environmental adaptation and quinoa domestication.

    DOI: 10.3389/fpls.2024.1434388

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  • QTL analysis of femaleness in monoecious spinach and fine mapping of a major QTL using an updated version of chromosome-scale pseudomolecules

    Yamano K., Haseda A., Iwabuchi K., Osabe T., Sudo Y., Pachakkil B., Tanaka K., Suzuki Y., Toyoda A., Hirakawa H., Onodera Y.

    PLoS ONE   19 ( 2 February )   e0296675   2024.2

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    Language:English   Publisher:PLoS ONE  

    Although spinach is predominantly dioecious, monoecious plants with varying proportions of female and male flowers are also present. Recently, monoecious inbred lines with highly female and male conditions have been preferentially used as parents for F1-hybrids, rather than dioecious lines. Accordingly, identifying the loci for monoecism is an important issue for spinach breeding. We here used long-read sequencing and Hi-C technology to construct SOL_r2.0_pseudomolecule, a set of six pseudomolecules of spinach chromosomes (total length: 879.2 Mb; BUSCO complete 97.0%) that are longer and more genetically complete than our previous version of pseudomolecules (688.0 Mb; 81.5%). Three QTLs, qFem2.1, qFem3.1, and qFem6.1, responsible for monoecism were mapped to SOL_r2.0_pseudomolecule. qFem3.1 had the highest LOD score and corresponded to the M locus, which was previously identified as a determinant of monoecious expression, by genetic analysis of progeny from female and monoecious plants. The other QTLs were shown to modulate the ratio of female to male flowers in monoecious plants harboring a dominant allele of the M gene. Our findings will enable breeders to efficiently produce highly female- and male-monoecious parental lines for F1-hybrids by pyramiding the three QTLs. Through fine-mapping, we narrowed the candidate region for the M locus to a 19.5 kb interval containing three protein-coding genes and one long non-coding RNA gene. Among them, only RADIALIS-like-2a showed a higher expression in the reproductive organs, suggesting that it might play a role in reproductive organogenesis. However, there is no evidence that it is involved in the regulation of stamen and pistil initiation, which are directly related to the floral sex differentiation system in spinach. Given that auxin is involved in reproductive organ formation in many plant species, genes related to auxin transport/response, in addition to floral organ formation, were identified as candidates for regulators of floral sex-differentiation from qFem2.1 and qFem6.1.

    DOI: 10.1371/journal.pone.0296675

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  • Comprehensive expression analysis of ERF transcription factors during chilling acclimation in Saintpaulia

    Kurata D., Fukutomi K., Kubo K., Shirasawa K., Hirakawa H., Hosokawa M.

    Plant Growth Regulation   2024   ISSN:01676903

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    Publisher:Plant Growth Regulation  

    Saintpaulia (Saintpaulia ionantha), a popular indoor ornamental potted plant, is native to the highlands of Kenya and Tanzania where temperatures rarely fall below 4 °C. Chilling injury during cultivation and transportation is a major commercial problem in Saintpaulia. In this study, we investigated chilling acclimation in Saintpaulia ‘Kilauea’. Plants grown at 20 °C (14 h light/10 h dark) displayed rapid and severe chilling injury after 24-h exposure to 4 °C. However, chilling injury at 4 °C could be dramatically reduced by pre-treating the plants at 10 °C but not at 6 °C. From whole genome analysis, 161 ethylene-responsive factors (ERFs) were identified and classified into 12 clades according to existing reports. Among these ERFs, 43, 8, and 4 ERFs were upregulated at 12, 24, and 48 h after 10 °C treatment, respectively. Most of these ERFs had GCC box and/or DRE/CRT core motifs-like sequences in their upstream regions. Finally, we compared the expression of ERFs between the treatments for 24 h at 10 °C, an effective temperature for chilling acclimation, and 6 °C, an ineffective temperature. The results showed that the expression of all six ERFs we investigated was increased by the 10 °C treatment, but not or only barely increased by the 6 °C treatment. This study suggests that Saintpaulia, a subtropical plant, can acclimate to low temperatures and that ERF upregulation is involved in chilling acclimation.

    DOI: 10.1007/s10725-024-01181-7

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  • Haplotype-resolved de novo genome assemblies of four coniferous tree species

    Shirasawa K., Mishima K., Hirakawa H., Hirao T., Tsubomura M., Nagano S., Iki T., Isobe S., Takahashi M.

    Journal of Forest Research   29 ( 2 )   151 - 157   2024   ISSN:13416979

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    Publisher:Journal of Forest Research  

    Coniferous trees in gymnosperm are an important source of wood production. Because of their long lifecycle, the breeding programs of coniferous tree are time- and labor-consuming. Genomics could accelerate the selection of superior trees or clones in the breeding programs; however, the genomes of coniferous trees are generally giant in size and exhibit high heterozygosity. Therefore, the generation of long contiguous genome assemblies of coniferous species has been difficult. In this study, we employed high-fidelity (HiFi) long-read sequencing technology to sequence and assemble the genomes of four coniferous tree species, Larix kaempferi, Chamaecyparis obtusa, Cryptomeria japonica, and Cunninghamia lanceolata. Genome assemblies of the four species totaled 13.5 Gb (L. kaempferi), 8.5 Gb (C. obtusa), 9.2 Gb (C. japonica), and 11.7 Gb (C. lanceolata), which covered 99.6% of the estimated genome sizes on average. The contig N50 value, which indicates assembly contiguity, ranged from 1.2 Mb in C. obtusa to 16.0 Mb in L. kaempferi, and the assembled sequences contained, on average, 89.2% of the single-copy orthologs conserved in embryophytes. Assembled sequences representing alternative haplotypes covered 70.3–95.1% of the genomes, suggesting that the four coniferous tree genomes exhibit high heterozygosity levels. The genome sequence information obtained in this study represents a milestone in tree genetics and genomics, and will facilitate gene discovery, allele mining, phylogenetics, and evolutionary studies in coniferous trees, and accelerate forest tree breeding programs.

    DOI: 10.1080/13416979.2023.2267304

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  • Pan genome of strawberry cultivars in Japan

    Isobe S., Shirasawa K., Hirakawa H., Hamano M., Ryu K., Kurokura T.

    Acta Horticulturae   1381   15 - 18   2023.11   ISSN:05677572

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    Publisher:Acta Horticulturae  

    Strawberry (Fragaria × ananassa) is an octoploid species with an estimated genome size of about 800 Mb. The entire genomes of seven strawberry cultivars, ‘Donner’, ‘Hokowase’, ‘Aiberry’, ‘Toyonoka’, ‘Sachinoka’, ‘Reikou’ and ‘Nyoho’, were sequenced in order to clarify the differences in genome structures among the cultivars bred in Japan. Genome sequences were obtained using PacBio Sequel II with one SMRT cell for each cultivar. The total lengths of the generated HiFi reads ranged from 23.1 to 31.4 Gb, representing 29-37x of the strawberry genome. De novo assembly was performed using Hifiasm. Total lengths of assembled primary contigs ranged from 820 to 929 Mb with N50 lengths of 16.6-26.0 Mb. Meanwhile, sum lengths of primary and haplotig contigs ranged from 1,334.3 (‘Nyoho’) to 1,520.2 Mb (‘Aiberry’). Ratios of haplotig contigs against the total length of primary and haplotig contigs ranged from 37% (‘Hokowase’) to 46% (‘Aiberry’). The top 50 primary contig sequences in the length of ‘Reikou’ were compared with the previously reported haploid pseudomolecule sequences of ‘Reikou’ (FAN_r2.3, a-haploid). One-to-one correspondences were observed between many primary contig sequences and FAN_r2.3 sequences, indicating the presence of primary contig sequences assembled at the chromosomal level. The pan genomes obtained in this study will contribute to identification of genome structure differences among all strawberries, including those tested here.

    DOI: 10.17660/ActaHortic.2023.1381.2

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  • Establishing a comprehensive web-based analysis platform forNicotiana benthamianagenome and transcriptome

    Ken-ichi Kurotani, Hideki Hirakawa, Kenta Shirasawa, Koya Tagiri, Moe Mori, Yasunori Ichihashi, Takamasa Suzuki, Yasuhiro Tanizawa, Yasukazu Nakamura, Sachiko Isobe, Michitaka Notaguchi

    2023.9

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  • Transcriptome analysis of tomato plants following salicylic acid-induced immunity against Clavibacter michiganensis ssp. michiganensis Reviewed

    Naoki Yokotani, Yoshinori Hasegawa, Yusuke Kouzai, Hideki Hirakawa, Sachiko Isobe

    Plant Biotechnology   40 ( 4 )   273 - 282   2023.9   ISSN:13424580

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.5511/plantbiotechnology.23.0711a

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  • Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species. International journal

    Hisako Ichihara, Manabu Yamada, Mitsuyo Kohara, Hideki Hirakawa, Andrea Ghelfi, Takuro Tamura, Akihiro Nakaya, Yasukazu Nakamura, Sachiko Shirasawa, Samatchaya Yamashita, Yosuke Toda, Daijiro Harada, Tsunakazu Fujishiro, Akiko Komaki, Jeffrey A Fawcett, Eiji Sugihara, Satoshi Tabata, Sachiko N Isobe

    BMC plant biology   23 ( 1 )   391 - 391   2023.8

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    BACKGROUND: Plant genome information is fundamental to plant research and development. Along with the increase in the number of published plant genomes, there is a need for an efficient system to retrieve various kinds of genome-related information from many plant species across plant kingdoms. Various plant databases have been developed, but no public database covers both genomic and genetic resources over a wide range of plant species. MAIN BODY: We have developed a plant genome portal site, Plant GARDEN (Genome And Resource Database Entry: https://plantgarden.jp/en/index ), to provide diverse information related to plant genomics and genetics in divergent plant species. Elasticsearch is used as a search engine, and cross-keyword search across species is available. Web-based user interfaces (WUI) for PCs and tablet computers were independently developed to make data searches more convenient. Several types of data are stored in Plant GARDEN: reference genomes, gene sequences, PCR-based DNA markers, trait-linked DNA markers identified in genetic studies, SNPs, and in/dels on publicly available sequence read archives (SRAs). The data registered in Plant GARDEN as of March 2023 included 304 assembled genome sequences, 11,331,614 gene sequences, 419,132 DNA markers, 8,225 QTLs, and 5,934 SNP lists (gvcf files). In addition, we have re-annotated all the genes registered in Plant GARDEN by using a functional annotation tool, Hayai-Annotation, to compare the orthologous relationships among genes. CONCLUSION: The aim of Plant GARDEN is to provide plant genome information for use in the fields of plant science as well as for plant-based industries, education, and other relevant areas. Therefore, we have designed a WUI that allows a diverse range of users to access such information in an easy-to-understand manner. Plant GARDEN will eventually include a wide range of plant species for which genome sequences are assembled, and thus the number of plant species in the database will continue to expand. We anticipate that Plant GARDEN will promote the understanding of genomes and gene diversity by facilitating comparisons of the registered sequences.

    DOI: 10.1186/s12870-023-04392-8

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  • Genome sequencing reveals the genetic architecture of heterostyly and domestication history of common buckwheat. International journal

    Jeffrey A Fawcett, Ryoma Takeshima, Shinji Kikuchi, Euki Yazaki, Tomoyuki Katsube-Tanaka, Yumei Dong, Meifang Li, Harriet V Hunt, Martin K Jones, Diane L Lister, Takanori Ohsako, Eri Ogiso-Tanaka, Kenichiro Fujii, Takashi Hara, Katsuhiro Matsui, Nobuyuki Mizuno, Kazusa Nishimura, Tetsuya Nakazaki, Hiroki Saito, Naoko Takeuchi, Mariko Ueno, Daiki Matsumoto, Miyu Norizuki, Kenta Shirasawa, Chengyun Li, Hideki Hirakawa, Tatsuya Ota, Yasuo Yasui

    Nature plants   9 ( 8 )   1236 - 1251   2023.8

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    Common buckwheat, Fagopyrum esculentum, is an orphan crop domesticated in southwest China that exhibits heterostylous self-incompatibility. Here we present chromosome-scale assemblies of a self-compatible F. esculentum accession and a self-compatible wild relative, Fagopyrum homotropicum, together with the resequencing of 104 wild and cultivated F. esculentum accessions. Using these genomic data, we report the roles of transposable elements and whole-genome duplications in the evolution of Fagopyrum. In addition, we show that (1) the breakdown of heterostyly occurs through the disruption of a hemizygous gene jointly regulating the style length and female compatibility and (2) southeast Tibet was involved in common buckwheat domestication. Moreover, we obtained mutants conferring the waxy phenotype for the first time in buckwheat. These findings demonstrate the utility of our F. esculentum assembly as a reference genome and promise to accelerate buckwheat research and breeding.

    DOI: 10.1038/s41477-023-01474-1

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  • Genome Sequence and Analysis of Nicotiana benthamiana, the Model Plant for Interactions between Organisms.

    Ken-Ichi Kurotani, Hideki Hirakawa, Kenta Shirasawa, Yasuhiro Tanizawa, Yasukazu Nakamura, Sachiko Isobe, Michitaka Notaguchi

    Plant & cell physiology   64 ( 2 )   248 - 257   2023.2   ISSN:00320781

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    Nicotiana benthamiana is widely used as a model plant for dicotyledonous angiosperms. In fact, the strains used in research are highly susceptible to a wide range of viruses. Accordingly, these strains are subject to plant pathology and plant-microbe interactions. In terms of plant-plant interactions, N. benthamiana is one of the plants that exhibit grafting affinity with plants from different families. Thus, N. benthamiana is a good model for plant biology and has been the subject of genome sequencing analyses for many years. However, N. benthamiana has a complex allopolyploid genome, and its previous reference genome is fragmented into 141,000 scaffolds. As a result, molecular genetic analysis is difficult to perform. To improve this effort, de novo whole-genome assembly was performed in N. benthamiana with Hifi reads, and 1,668 contigs were generated with a total length of 3.1 Gb. The 21 longest scaffolds, regarded as pseudomolecules, contained a 2.8-Gb sequence, occupying 95.6% of the assembled genome. A total of 57,583 high-confidence gene sequences were predicted. Based on a comparison of the genome structures between N. benthamiana and N. tabacum, N. benthamiana was found to have more complex chromosomal rearrangements, reflecting the age of interspecific hybridization. To verify the accuracy of the annotations, the cell wall modification genes involved in grafting were analyzed, which revealed not only the previously indeterminate untranslated region, intron and open reading frame sequences but also the genomic locations of their family genes. Owing to improved genome assembly and annotation, N. benthamiana would increasingly be more widely accessible.

    DOI: 10.1093/pcp/pcac168

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  • The genome of Lyophyllum shimeji provides insight into the initial evolution of ectomycorrhizal fungal genomes. International journal

    Yuuki Kobayashi, Tomoko F Shibata, Hideki Hirakawa, Tomoaki Nishiyama, Akiyoshi Yamada, Mitsuyasu Hasebe, Shuji Shigenobu, Masayoshi Kawaguchi

    DNA research : an international journal for rapid publication of reports on genes and genomes   30 ( 1 )   2023.2   ISSN:1340-2838 eISSN:1756-1663

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    Mycorrhizae are one of the most fundamental symbioses between plants and fungi, with ectomycorrhizae being the most widespread in boreal forest ecosystems. Ectomycorrhizal fungi are hypothesized to have evolved convergently from saprotrophic ancestors in several fungal clades, especially members of the subdivision Agaricomycotina. Studies on fungal genomes have identified several typical characteristics of mycorrhizal fungi, such as genome size expansion and decreases in plant cell-wall degrading enzymes (PCWDEs). However, genomic changes concerning the evolutionary transition to the ectomycorrhizal lifestyle are largely unknown. In this study, we sequenced the genome of Lyophyllum shimeji, an ectomycorrhizal fungus that is phylogenetically related to saprotrophic species and retains some saprotroph-like traits. We found that the genome of Ly. shimeji lacks both incremental increases in genome size and reduced numbers of PCWDEs. Our findings suggest that the previously reported common genomic traits of mycorrhizal fungi are not essential for the ectomycorrhizal lifestyle but are a result of abolishing saprotrophic activity. Since Ly. shimeji is commercially consumed as an edible mushroom, the newly available genomic information may also impact research designed to enhance the cultivation of this mushroom.

    DOI: 10.1093/dnares/dsac053

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  • An improved reference genome for Trifolium subterraneum L. provides insight into molecular diversity and intra-specific phylogeny. International journal

    Kenta Shirasawa, Roger Moraga, Andrea Ghelfi, Hideki Hirakawa, Hideki Nagasaki, Kioumars Ghamkhar, Brent A Barrett, Andrew G Griffiths, Sachiko N Isobe

    Frontiers in plant science   14   1103857 - 1103857   2023   ISSN:1664-462X

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    Subterranean clover (Trifolium subterraneum L., Ts) is a geocarpic, self-fertile annual forage legume with a compact diploid genome (n = x = 8, 544 Mb/1C). Its resilience and climate adaptivity have made it an economically important species in Mediterranean and temperate zones. Using the cultivar Daliak, we generated higher resolution sequence data, created a new genome assembly TSUd_3.0, and conducted molecular diversity analysis for copy number variant (CNV) and single-nucleotide polymorphism (SNP) among 36 cultivars. TSUd_3.0 substantively improves prior genome assemblies with new Hi-C and long-read sequence data, covering 531 Mb, containing 41,979 annotated genes and generating a 94.4% BUSCO score. Comparative genomic analysis among select members of the tribe Trifolieae indicated TSUd 3.0 corrects six assembly-error inversion/duplications and confirmed phylogenetic relationships. Its synteny with T. pratense, T. repens, Medicago truncatula and Lotus japonicus genomes were assessed, with the more distantly related T. repens and M. truncatula showing higher levels of co-linearity with Ts than between Ts and its close relative T. pratense. Resequencing of 36 cultivars discovered 7,789,537 SNPs subsequently used for genomic diversity assessment and sequence-based clustering. Heterozygosity estimates ranged from 1% to 21% within the 36 cultivars and may be influenced by admixture. Phylogenetic analysis supported subspecific genetic structure, although it indicates four or five groups, rather than the three recognized subspecies. Furthermore, there were incidences where cultivars characterized as belonging to a particular subspecies clustered with another subspecies when using genomic data. These outcomes suggest that further investigation of Ts sub-specific classification using molecular and morpho-physiological data is needed to clarify these relationships. This upgraded reference genome, complemented with comprehensive sequence diversity analysis of 36 cultivars, provides a platform for future gene functional analysis of key traits, and genome-based breeding strategies for climate adaptation and agronomic performance. Pangenome analysis, more in-depth intra-specific phylogenomic analysis using the Ts core collection, and functional genetic and genomic studies are needed to further augment knowledge of Trifolium genomes.

    DOI: 10.3389/fpls.2023.1103857

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  • Whole-genome sequence analysis of mutations in rice plants regenerated from zygotes, mature embryos, and immature embryos

    Ichikawa Masako, Kato Norio, Toda Erika, Kashihara Masakazu, Ishida Yuji, Hiei Yukoh, Isobe Sachiko N., Shirasawa Kenta, Hirakawa Hideki, Okamoto Takashi, Komari Toshihiko

    Breeding Science   73 ( 3 )   349 - 353   2023   ISSN:13447610 eISSN:13473735

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    Language:English   Publisher:Japanese Society of Breeding  

    <p>Somaclonal variation was studied by whole-genome sequencing in rice plants (<i>Oryza sativa</i> L., ‘Nipponbare’) regenerated from the zygotes, mature embryos, and immature embryos of a single mother plant. The mother plant and its seed-propagated progeny were also sequenced. A total of 338 variants of the mother plant sequence were detected in the progeny, and mean values ranged from 9.0 of the seed-propagated plants to 37.4 of regenerants from mature embryos. The natural mutation rate of 1.2 × 10<sup>–8</sup> calculated using the variants in the seed-propagated plants was consistent with the values reported previously. The ratio of single nucleotide variants (SNVs) among the variants in the seed-propagated plants was 91.1%, which is higher than 56.1% previously reported, and not significantly different from those in the regenerants. Overall, the ratio of transitions to transversions of SNVs was lower in the regenerants as shown previously. Plants regenerated from mature embryos had significantly more variants than different progeny types. Therefore, using zygotes and immature embryos can reduce somaclonal variation during the genetic manipulation of rice.</p>

    DOI: 10.1270/jsbbs.22100

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  • Haploid-resolved and chromosome-scale genome assembly in hexa-autoploid sweetpotato (Ipomoea batatas(L.) Lam)

    Ung-Han Yoon, Qinghe Cao, Kenta Shirasawa, Hong Zhai, Tae-Ho Lee, Masaru Tanaka, Hideki Hirakawa, Jang-Ho Hahn, Xiangfeng Wang, Ho Soo Kim, Hiroaki Tabuchi, An Zhang, Tae-Ho Kim, Hideki Nagasaki, Shizhuo Xiao, Yoshihiro Okada, Jae Cheol Jeong, Soichiro Nagano, Younhee Shin, Hyeong-Un Lee, Sul-U Park, Seung Jae Lee, Keunpyo Lee, Jung-Wook Yang, Byoung Ohg Ahn, Daifu Ma, Yasuhiro Takahata, Sang-Soo Kwak, Qingchang Liu, Sachiko Isobe

    育種学研究   25   2022.12   ISSN:1344-7629

  • Chromosome-scale genome assembly of <i>Eustoma grandiflorum</i>, the first complete genome sequence in the genus <i>Eustoma</i> International journal

    Kenta Shirasawa, Ryohei Arimoto, Hideki Hirakawa, Motoyuki Ishimorai, Andrea Ghelfi, Masami Miyasaka, Makoto Endo, Saneyuki Kawabata, Sachiko N Isobe

    G3 Genes|Genomes|Genetics   13 ( 2 )   2022.12   eISSN:2160-1836

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    Eustoma grandiflorum (Raf.) Shinn. is an annual herbaceous plant native to the southern United States, Mexico, and the Greater Antilles. It has a large flower with a variety of colors and is an important flower crop. In this study, we established a chromosome-scale de novo assembly of E. grandiflorum genome sequences by integrating four genomic and genetic approaches: (1) Pacific Biosciences (PacBio) Sequel deep sequencing, (2) error correction of the assembly by Illumina short reads, (3) scaffolding by chromatin conformation capture sequencing (Hi-C), and (4) genetic linkage maps derived from an F2 mapping population. Thirty-six pseudomolecules and 64 unplaced scaffolds were created, with a total length of 1,324.8 Mb. A total of 36,619 genes were predicted on the genome as high-confidence genes. A comparison of genome structure between E. grandiflorum and C. canephora or O. pumila suggested whole genome duplication after divergence between the families Gentianaceae and Rubiaceae. Phylogenetic analysis with single-copy genes suggested that the divergence time between Gentianaceae and Rubiaceae was 74.94 MYA. Genetic diversity analysis was performed for nine commercial E. grandiflorum varieties bred in Japan, from which 254,205 variants were identified. This first report of the construction of a reference genome sequence in genus Eustoma is expected to contribute to genetic and genomic studies in this genus and in the family Gentianaceae.

    DOI: 10.1093/g3journal/jkac329

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  • Genome assembly and transcriptomic analyses of the repeatedly rejuvenating jellyfish Turritopsis dohrnii. International journal

    Yoshinori Hasegawa, Takashi Watanabe, Reo Otsuka, Shigenobu Toné, Shin Kubota, Hideki Hirakawa

    DNA research : an international journal for rapid publication of reports on genes and genomes   30 ( 1 )   2022.12   ISSN:13402838

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    Only two hydromedusan species, Turritopsis dohrnii and T. sp., have exhibited experimental multiple-repeat life cycle reversion in the laboratory, which can be artificially induced by various means such as incubation with CsCl, heat shock, and mechanical damage with needles. In the present study, we constructed a genome assembly of T. dohrnii using Pacific Biosciences long-reads and Illumina short-reads, for which the genome DNA was extracted from 1500 young medusae originated from a single clone. The total length of the draft genome sequence of T. dohrnii was 435.9 Mb (N50 length 747.2 kb). We identified 23,314 high-confidence genes and found the characteristics of RNA expression among developmental stages. Our genome assembly and transcriptome data provide a key model system resource that will be useful for understanding cyclical rejuvenation.

    DOI: 10.1093/dnares/dsac047

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  • Chromosome-scale genome assembly of Glycyrrhiza uralensis revealed metabolic gene cluster centred specialized metabolites biosynthesis. International journal

    Amit Rai, Hideki Hirakawa, Megha Rai, Yohei Shimizu, Kenta Shirasawa, Shinji Kikuchi, Hikaru Seki, Mami Yamazaki, Atsushi Toyoda, Sachiko Isobe, Toshiya Muranaka, Kazuki Saito

    DNA research : an international journal for rapid publication of reports on genes and genomes   29 ( 6 )   2022.12   ISSN:13402838

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    A high-quality genome assembly is imperative to explore the evolutionary basis of characteristic attributes that define chemotype and provide essential resources for a molecular breeding strategy for enhanced production of medicinal metabolites. Here, using single-molecule high-fidelity (HiFi) sequencing reads, we report chromosome-scale genome assembly for Chinese licorice (Glycyrrhiza uralensis), a widely used herbal and natural medicine. The entire genome assembly was achieved in eight chromosomes, with contig and scaffold N50 as 36.02 and 60.2 Mb, respectively. With only 17 assembly gaps and half of the chromosomes having no or one assembly gap, the presented genome assembly is among the best plant genomes to date. Our results showed an advantage of using highly accurate long-read HiFi sequencing data for assembling a highly heterozygous genome including its complexed repeat content. Additionally, our analysis revealed that G. uralensis experienced a recent whole-genome duplication at approximately 59.02 million years ago post a gamma (γ) whole-genome triplication event, which contributed to its present chemotype features. The metabolic gene cluster analysis identified 355 gene clusters, which included the entire biosynthesis pathway of glycyrrhizin. The genome assembly and its annotations provide an essential resource for licorice improvement through molecular breeding and the discovery of valuable genes for engineering bioactive components and understanding the evolution of specialized metabolites biosynthesis.

    DOI: 10.1093/dnares/dsac043

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  • De novo whole-genome assembly in an interspecific hybrid table grape, 'Shine Muscat'. International journal

    Kenta Shirasawa, Hideki Hirakawa, Akifumi Azuma, Fumiya Taniguchi, Toshiya Yamamoto, Akihiko Sato, Andrea Ghelfi, Sachiko N Isobe

    DNA research : an international journal for rapid publication of reports on genes and genomes   29 ( 6 )   2022.12   ISSN:13402838

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    The first genome sequence of an interspecific grape hybrid (Vitis labruscana × Vitis vinifera), 'Shine Muscat', an elite table grape cultivar bred in Japan, is presented. The resultant genome assemblies included two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a 'pseudo-haploid' genome. The unphased sequences, assembled to the chromosome level with Hi-C reads, spanned 488.97 Mb in length, 99.1% of the estimated genome size, with 4,595 scaffold sequences and a 23.9-Mb N50 length. The phased sequences had 15,650 scaffolds spanning 1.0 Gb and a 4.2-Mb N50 length. 32,827 high-confidence genes were predicted on the unphased genomes. Clustering analysis of the 'Shine Muscat' gene sequences with three other Vitis species and Arabidopsis indicated that 11,279 orthologous gene clusters were common to Vitis spp. and Arabidopsis, 4,385 were Vitis specific, and 234 were 'Shine Muscat' specific. Whole-genome resequencing was also performed for the parental lines of 'Shine Muscat', Akitsu-21 and 'Hakunan', and parental-specific copy number variations were identified. The obtained genome resources provide new insights that could assist in cultivation and breeding strategies to produce high-quality table grapes.

    DOI: 10.1093/dnares/dsac040

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  • Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica) International journal

    Kentaro Mishima, Hideki Hirakawa, Taiichi Iki, Yoko Fukuda, Tomonori Hirao, Akira Tamura, Makoto Takahashi

    BMC Plant Biology   22 ( 1 )   470 - 470   2022.10   eISSN:1471-2229

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    Abstract

    Background

    Japanese larch (Larix kaempferi) is an economically important deciduous conifer species that grows in cool-temperate forests and is endemic to Japan. Kuril larch (L. gmelinii var. japonica) is a variety of Dahurian larch that is naturally distributed in the Kuril Islands and Sakhalin. The hybrid larch (L. gmelinii var. japonica × L. kaempferi) exhibits heterosis, which manifests as rapid juvenile growth and high resistance to vole grazing. Since these superior characteristics have been valued by forestry managers, the hybrid larch is one of the most important plantation species in Hokkaido. To accelerate molecular breeding in these species, we collected and compared full-length cDNA isoforms (Iso-Seq) and RNA-Seq short-read, and merged them to construct candidate gene as reference for both Larix species. To validate the results, candidate protein-coding genes (ORFs) related to some flowering signal-related genes ​were screened from the reference sequences, and the phylogenetic relationship with closely related species was elucidated.

    Results

    Using the isoform sequencing of PacBio RS ll and the de novo assembly of RNA-Seq short-read sequences, we identified 50,690 and 38,684 ORFs in Japanese larch and Kuril larch, respectively. BUSCO completeness values were 90.5% and 92.1% in the Japanese and Kuril larches, respectively. After comparing the collected ORFs from the two larch species, a total of 19,813 clusters, comprising 22,571 Japanese larch ORFs and 22,667 Kuril larch ORFs, were contained in the intersection of the Venn diagram. In addition, we screened several ORFs related to flowering signals (SUPPRESSER OF OVEREXPRESSION OF CO1: SOC1, LEAFY: LFY, FLOWERING Locus T: FT, CONSTANCE: CO) from both reference sequences, and very similar found in other species.

    Conclusions

    The collected ORFs will be useful as reference sequences for molecular breeding of Japanese and Kuril larches, and also for clarifying the evolution of the conifer genome and investigating functional genomics.

    DOI: 10.1186/s12870-022-03862-9

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    Other Link: https://link.springer.com/article/10.1186/s12870-022-03862-9/fulltext.html

  • 20 未利用地から農地への転換に伴う土壌微生物群集構造変化の解析(関西支部講演会 2021年度支部講演会)

    高田 理江, 花野 滋, 宮本 託志, 滝澤 理仁, 冨永 逹, 柴田 大輔, 櫻井 望, 平川 英樹, 小林 優

    日本土壌肥料学会講演要旨集   68   201 - 201   2022.9   ISSN:0288-5840 eISSN:2424-0575

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    Language:Japanese   Publisher:一般社団法人 日本土壌肥料学会  

    DOI: 10.20710/dohikouen.68.0_201_2

    CiNii Research

  • Widespread and transgenerational retrotransposon activation in inter‐ and intraspecies recombinant inbred populations of <i>Lotus japonicus</i> International journal

    Eigo Fukai, Manabu Yoshikawa, Niraj Shah, Niels Sandal, Akio Miyao, Seijiro Ono, Hideki Hirakawa, Turgut Yigit Akyol, Yosuke Umehara, Ken‐Ichi Nonomura, Jens Stougaard, Hirohiko Hirochika, Makoto Hayashi, Shusei Sato, Stig Uggerhøj Andersen, Keiichi Okazaki

    The Plant Journal   111 ( 5 )   1397 - 1410   2022.9   ISSN:0960-7412 eISSN:1365-313X

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    Transposable elements (TEs) constitute a large proportion of genomes of multicellular eukaryotes, including flowering plants. TEs are normally maintained in a silenced state and their transpositions rarely occur. Hybridization between distant species has been regarded as a 'shock' that stimulates genome reorganization, including TE mobilization. However, whether crosses between genetically close parents that result in viable and fertile offspring can induce TE transpositions has remained unclear. Here, we investigated the activation of long terminal repeat (LTR) retrotransposons in three Lotus japonicus recombinant inbred line (RIL) populations. We found that at least six LTR retrotransposon families were activated and transposed in 78% of the RILs investigated. LORE1a, one of the transposed LTR retrotransposons, showed transgenerational epigenetic activation, indicating the long-term effects of epigenetic instability induced by hybridization. Our study highlights TE activation as an unexpectedly common event in plant reproduction.

    DOI: 10.1111/tpj.15896

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    Other Link: https://onlinelibrary.wiley.com/doi/full-xml/10.1111/tpj.15896

  • Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping International journal

    Daisuke Sekine, Satoshi Oku, Tsukasa Nunome, Hideki Hirakawa, Mai Tsujimura, Toru Terachi, Atsushi Toyoda, Masayoshi Shigyo, Shusei Sato, Hikaru Tsukazaki

    DNA Research   29 ( 5 )   2022.8   ISSN:13402838 eISSN:1756-1663

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    Abstract

    Onions are one of the most widely cultivated vegetables worldwide; however, the development and utilization of molecular markers have been limited because of the large genome of this plant. We present a genome-wide marker design workflow for onions and its application in a high-throughput genotyping method based on target amplicon sequencing. The efficiency of the method was evaluated by genotyping of F2 populations. In the marker design workflow, unigene and genomic sequence data sets were constructed, and polymorphisms between parental lines were detected through transcriptome sequence analysis. The positions of polymorphisms detected in the unigenes were mapped onto the genome sequence, and primer sets were designed. In total, 480 markers covering the whole genome were selected. By genotyping an F2 population, 329 polymorphic sites were obtained from the estimated positions or the flanking sequences. However, missing or sparse marker regions were observed in the resulting genetic linkage map. We modified the markers to cover these regions by genotyping the other F2 populations. The grouping and order of markers on the linkages were similar across the genetic maps. Our marker design workflow and target amplicon sequencing are useful for genome-wide genotyping of onions owing to their reliability, cost effectiveness, and flexibility.

    DOI: 10.1093/dnares/dsac020

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  • Plant GARDEN: a portal website for accessing plant genome, DNA marker, and SNP information

    H. Ichihara, H. Hirakawa, A. Ghelfi, M. Kohara, M. Yamada, T. Tamura, A. Nakaya, Y. Nakamura, S. Shirasawa, E. Sugihara, S. Tabata, S. Isobe

    Acta Horticulturae   1339 ( 1339 )   415 - 418   2022.4   ISSN:0567-7572 eISSN:2406-6168

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    Publishing type:Research paper (scientific journal)   Publisher:International Society for Horticultural Science (ISHS)  

    DOI: 10.17660/actahortic.2022.1339.52

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  • A genome-wide association and fine-mapping study of white rust resistance in hexaploid chrysanthemum cultivars with a wild diploid reference genome. International journal

    Katsuhiko Sumitomo, Kenta Shirasawa, Sachiko Isobe, Hideki Hirakawa, Akiho Harata, Michiharu Nakano, Yoshihiro Nakano, Masafumi Yagi, Tamotsu Hisamatsu, Hiroyasu Yamaguchi, Fumiya Taniguchi

    Horticulture research   9   uhac170   2022   ISSN:26626810

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    White rust caused by Puccinia horiana is one of the most serious diseases of chrysanthemum (Chrysanthemum × morifolium). In this study, we report the DNA markers associated with resistance against P. horiana via a simple approach using the genome of a wild diploid relative, Chrysanthemum seticuspe. First, we identified the important region of the genome in the resistant cultivar "Ariesu" via a genome-wide association study. Simplex single nucleotide polymorphism (SNP) markers mined from ddRAD-Seq were used in a biparental population originating from crosses between resistant "Ariesu" and susceptible "Yellow Queen". The C. seticuspe genome was used as a reference. For the fine mapping of P. horiana resistance locus 2 (Phr2), a comparative whole genome sequencing study was conducted. Although the genome sequences of chrysanthemum cultivars assembled via the short-read approach were fragmented, reliable genome alignments were reconstructed by mapping onto the chromosome level of the C. seticuspe pseudomolecule. Base variants were then identified by comparing the assembled genome sequences of resistant "Ariesu" and susceptible "Yellow Queen". Consequently, SNP markers that were closer to Phr2 compared with ddRAD-Seq markers were obtained. These SNP markers co-segregated with resistance in F1 progenies originating from resistant "Ariesu" and showed robust transferability for detecting Phr2-conferring resistance among chrysanthemum genetic resources. The wild C. seticuspe pseudomolecule, a de facto monoploid genome used for ddRAD-Seq analysis and assembled genome sequence comparison, demonstrated this method's utility as a model for developing DNA markers in hexaploid chrysanthemum cultivars.

    DOI: 10.1093/hr/uhac170

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  • Construction of a high-density linkage map and graphical representation of the arrangement of transcriptome-based unigene markers on the chromosomes of onion, Allium cepa L. International journal

    Satoshi Fujito, Turgut Yigit Akyol, Takuya Mukae, Tadayuki Wako, Ken-ichiro Yamashita, Hikaru Tsukazaki, Hideki Hirakawa, Keisuke Tanaka, Yoko Mine, Shusei Sato, Masayoshi Shigyo

    BMC Genomics   22 ( 1 )   481 - 481   2021.12   eISSN:1471-2164

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    <title>Abstract</title><sec>
    <title>Background</title>
    Genomic information for <italic>Allium cepa</italic> L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of <italic>A. fistulosum</italic> L.-<italic>A. cepa</italic> monosomic addition lines (MALs) and doubled haploids (DHs). These were the parental lines of an <italic>A. cepa</italic> mapping population for transcriptome-based SNP genotyping.


    </sec><sec>
    <title>Results</title>
    We mapped the transcriptome sequence reads from a series of <italic>A. fistulosum</italic>-<italic>A. cepa</italic> MALs onto the unigene sequence of the doubled haploid shallot <italic>A. cepa</italic> Aggregatum group (DHA) and compared the MAL genotype call for parental bunching onion and shallot transcriptome mapping data. We identified SNP sites with at least four reads on 25,462 unigenes. They were anchored on eight <italic>A. cepa</italic> chromosomes. A single SNP site was identified on 3,278 unigenes and multiple SNPs were identified on 22,184 unigenes. The chromosome marker information was made public via the web database Allium TDB (<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://alliumtdb.kazusa.or.jp/">http://alliumtdb.kazusa.or.jp/</ext-link>). To apply transcriptome based genotyping approach for genetic mapping, we gathered RNA sequence data from 96 lines of a DHA × doubled haploid bulb onion <italic>A. cepa</italic> common onion group (DHC) mapping population. After selecting co-dominant SNP sites, 16,872 SNPs were identified in 5,339 unigenes. Of these, at least two SNPs with identical genotypes were found in 1,435 unigenes. We developed a linkage map using genotype information from these unigenes. All unigene markers mapped onto the eight chromosomes and graphical genotyping was conducted based on the unigene order information. Another 2,963 unigenes were allocated onto the eight chromosomes. To confirm the accuracy of this transcriptome-based genetic linkage map, conventional PCR-based markers were used for linkage analysis. All SNP - and PCR-based markers were mapped onto the expected linkage groups and no inconsistency was found among these chromosomal locations.


    </sec><sec>
    <title>Conclusions</title>
    Effective transcriptome analysis with unique <italic>Allium</italic> resources successfully associated numerous chromosome markers with unigene information and a high-density <italic>A. cepa</italic> linkage map. The information on these unigene markers is valuable in genome sequencing and useful trait detection in <italic>Allium</italic>.


    </sec>

    DOI: 10.1186/s12864-021-07803-y

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  • Transcriptome analysis of Clavibacter michiganensis subsp. michiganensis-infected tomatoes: a role of salicylic acid in the host response International journal

    Naoki Yokotani, Yoshinori Hasegawa, Masaru Sato, Hideki Hirakawa, Yusuke Kouzai, Yoko Nishizawa, Eiji Yamamoto, Yoshiki Naito, Sachiko Isobe

    BMC Plant Biology   21 ( 1 )   476 - 476   2021.12   eISSN:1471-2229

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    <title>Abstract</title>Bacterial canker of tomato (<italic>Solanum lycopersicon</italic>) caused by the Gram-positive bacterium <italic>Clavibacter michiganensis</italic> subsp. <italic>michiganensis</italic> (<italic>Cmm</italic>) is an economically important disease<italic>.</italic> To understand the host defense response to <italic>Cmm</italic> infection, transcriptome sequences in tomato cotyledons were analyzed by RNA-seq. Overall, 1788 and 540 genes were upregulated and downregulated upon infection, respectively. Gene Ontology enrichment analysis revealed that genes involved in the defense response, phosphorylation, and hormone signaling were over-represented by the infection. Induced expression of defense-associated genes suggested that the tomato response to <italic>Cmm</italic> showed similarities to common plant disease responses. After infection, many resistance gene analogs (RGAs) were transcriptionally upregulated, including the expressions of some receptor-like kinases (RLKs) involved in pattern-triggered immunity. The expressions of <italic>WRKYs</italic>, <italic>NACs</italic>, <italic>HSFs</italic>, and <italic>CBP60s</italic> encoding transcription factors (TFs) reported to regulate defense-associated genes were induced after infection with <italic>Cmm</italic>. Tomato genes orthologous to Arabidopsis <italic>EDS1</italic>, <italic>EDS5/SID1</italic>, and <italic>PAD4/EDS9</italic>, which are causal genes of salicylic acid (SA)-deficient mutants, were upregulated after infection with <italic>Cmm</italic>. Furthermore, <italic>Cmm</italic> infection drastically stimulated SA accumulation in tomato cotyledons. Genes involved in the phenylalanine ammonia lyase pathway were upregulated, whereas metabolic enzyme gene expression in the isochorismate synthase pathway remained unchanged. Exogenously applied SA suppressed bacterial growth and induced the expression of <italic>WRKYs</italic>, suggesting that some <italic>Cmm</italic>-responsive genes are regulated by SA signaling, and SA signaling activation should improve tomato immunity against <italic>Cmm</italic>.

    DOI: 10.1186/s12870-021-03251-8

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    Other Link: https://link.springer.com/article/10.1186/s12870-021-03251-8/fulltext.html

  • A chromosome-scale draft genome sequence of horsegram (Macrotyloma uniflorum)

    Kenta Shirasawa, Rakesh Chahota, Hideki Hirakawa, Soichiro Nagano, Hideki Nagasaki, Tilak Sharma, Sachiko Isobe

    Gigabyte   2021   1 - 23   2021.10   eISSN:2709-4715

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    DOI: 10.46471/gigabyte.30

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  • A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum. International journal

    Michiharu Nakano, Hideki Hirakawa, Eigo Fukai, Atsushi Toyoda, Rei Kajitani, Yohei Minakuchi, Takehiko Itoh, Yohei Higuchi, Toshiaki Kozuka, Hidemasa Bono, Kenta Shirasawa, Ippei Shiraiwa, Katsuhiko Sumitomo, Tamotsu Hisamatsu, Michio Shibata, Sachiko Isobe, Kenji Taniguchi, Makoto Kusaba

    Communications biology   4 ( 1 )   1167 - 1167   2021.10

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    Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the C. seticuspe genome. The genome contained more than 80% interspersed repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in C. seticuspe, contributing to arelatively large genome size. Furthermore, we identified a retrotransposon family, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in C. seticuspe. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing.

    DOI: 10.1038/s42003-021-02704-y

    PubMed

  • Genome features of common vetch ( Vicia sativa ) in natural habitats International journal

    Kenta Shirasawa, Shunichi Kosugi, Kazuhiro Sasaki, Andrea Ghelfi, Koei Okazaki, Atsushi Toyoda, Hideki Hirakawa, Sachiko Isobe

    Plant Direct   5 ( 10 )   e352   2021.10   ISSN:2475-4455 eISSN:2475-4455

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    Wild plants are often tolerant to biotic and abiotic stresses in their natural environments, whereas domesticated plants such as crops frequently lack such resilience. This difference is thought to be due to the high levels of genome heterozygosity in wild plant populations and the low levels of heterozygosity in domesticated crop species. In this study, common vetch (Vicia sativa) was used as a model to examine this hypothesis. The common vetch genome (2n = 14) was estimated as 1.8 Gb in size. Genome sequencing produced a reference assembly that spanned 1.5 Gb, from which 31,146 genes were predicted. Using this sequence as a reference, 24,118 single nucleotide polymorphisms were discovered in 1243 plants from 12 natural common vetch populations in Japan. Common vetch genomes exhibited high heterozygosity at the population level, with lower levels of heterozygosity observed at specific genome regions. Such patterns of heterozygosity are thought to be essential for adaptation to different environments. The resources generated in this study will provide insights into de novo domestication of wild plants and agricultural enhancement.

    DOI: 10.1002/pld3.352

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    Other Link: https://onlinelibrary.wiley.com/doi/full-xml/10.1002/pld3.352

  • Tracking an Introduced Arbuscular Mycorrhizal Fungus in Allium fistulosum in a Field Condition With or Without Controlling Indigenous Fungi by Soil Fumigation As Well as Evaluation on Plant Phosphorus and Growth Reviewed

    Takumi Sato, Rieko Niwa, Tatsuhiro Ezawa, Shusei Sato, Hideki Hirakawa, Shigenobu Yoshida, Weiguo Cheng, Keitaro Tawaraya

    Journal of Soil Science and Plant Nutrition   21 ( 4 )   2781 - 2790   2021.8   ISSN:0718-9508 eISSN:0718-9516

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    Increased plant phosphorus uptake and growth as a result of inoculation with arbuscular mycorrhizal (AM) fungi is observed less often under field conditions than in pot experiments. Interaction between introduced and indigenous AM fungi is one of the reasons for ineffectiveness of inoculation in the field. We aimed to distinguish the effect of introduced and indigenous AM fungi on phosphorus uptake and growth of Allium fistulosum in a field experiment. Superphosphate was applied in the ratio of 0 or 317 P kg ha(-1) to the plots fumigated with or without dazomet that is a common soil fumigant. Seedlings of A. fistulosum that had been inoculated with or without Rhizophagus spp. strain R-10 were transplanted into the plots. AM fungal colonization, OTU read abundance of indigenous and introduced AM fungi, shoot P concentration, and shoot growth were measured at 31, 60, 90, and 131 days after transplanting (DAT). We could partially separate the effects of introduced AM fungi from indigenous AM fungi by fumigation with dazomet. Though neither inoculation nor P level affected shoot fresh weight and shoot P content in the non-fumigated main plot at 131 DAT, significantly higher shoot fresh weight was obtained by the inoculation with no P fertilizer in the fumigated main plot at this final sampling stage. These results indicate that the colonization of roots by introduced AM fungi is affected by the abundance of indigenous AM fungi and this interaction determines growth response of host plants under field conditions.

    DOI: 10.1007/s42729-021-00565-2

    Web of Science

  • A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits. International journal

    Hideki Hirakawa, Atsushi Toyoda, Takehiko Itoh, Yutaka Suzuki, Atsushi J Nagano, Suguru Sugiyama, Yasuyuki Onodera

    DNA research : an international journal for rapid publication of reports on genes and genomes   28 ( 3 )   2021.6   ISSN:1340-2838

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    Spinach (Spinacia oleracea) is grown as a nutritious leafy vegetable worldwide. To accelerate spinach breeding efficiency, a high-quality reference genome sequence with great completeness and continuity is needed as a basic infrastructure. Here, we used long-read and linked-read technologies to construct a de novo spinach genome assembly, designated SOL_r1.1, which was comprised of 287 scaffolds (total size: 935.7 Mb; N50 = 11.3 Mb) with a low proportion of undetermined nucleotides (Ns = 0.34%) and with high gene completeness (BUSCO complete 96.9%). A genome-wide survey of resistance gene analogues identified 695 genes encoding nucleotide-binding site domains, receptor-like protein kinases, receptor-like proteins and transmembrane-coiled coil domains. Based on a high-density double-digest restriction-site associated DNA sequencing-based linkage map, the genome assembly was anchored to six pseudomolecules representing ∼73.5% of the whole genome assembly. In addition, we used SOL_r1.1 to identify quantitative trait loci for bolting timing and fruit/seed shape, which harbour biologically plausible candidate genes, such as homologues of the FLOWERING LOCUS T and EPIDERMAL PATTERNING FACTOR-LIKE genes. The new genome assembly, SOL_r1.1, will serve as a useful resource for identifying loci associated with important agronomic traits and for developing molecular markers for spinach breeding/selection programs.

    DOI: 10.1093/dnares/dsab004

    PubMed

  • Construction of a high-density genetic map from RNA-Seq data in <i>Pinus thunbergii</i>

    Hirao Tomonori, Hirakawa Hideki, Matsunaga Koji, Mishima Kentaro, Nose Mine

    The Japanese Forest Society Congress   132 ( 0 )   367   2021.5

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    <p>[in Japanese]</p>

    DOI: 10.11519/jfsc.132.0_367

    CiNii Research

  • Genomic region associated with pod color variation in pea (Pisum sativum). International journal

    Kenta Shirasawa, Kazuhiro Sasaki, Hideki Hirakawa, Sachiko Isobe

    G3 (Bethesda, Md.)   11 ( 5 )   2021.5

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    Pea (Pisum sativum) was chosen as the research material by Gregor Mendel to discover the laws of inheritance. Out of seven traits studied by Mendel, genes controlling three traits including pod shape, pod color, and flower position have not been identified to date. With the aim of identifying the genomic region controlling pod color, we determined the genome sequence of a pea line with yellow pods. Genome sequence reads obtained using a Nanopore sequencing technology were assembled into 117,981 contigs (3.3 Gb), with an N50 value of 51.2 kb. A total of 531,242 potential protein-coding genes were predicted, of which 519,349 (2.8 Gb) were located within repetitive sequences (2.8 Gb). The assembled sequences were ordered using a reference as a guide to build pseudomolecules. Subsequent genetic and association analyses led to the identification of a genomic region that controls pea pod color. DNA sequences at this genomic location and transcriptome profiles of green and yellow pod lines were analyzed, and genes encoding 3' exoribonucleases were selected as potential candidates controlling pod color. The results presented in this study are expected to accelerate pan-genome studies in pea and facilitate the identification of the gene controlling one of the traits studied by Mendel.

    DOI: 10.1093/g3journal/jkab081

    PubMed

  • Correction to: Effectiveness and safety of nivolumab in patients with head and neck cancer in Japanese real‑world clinical practice: a multicentre retrospective clinical study.

    Hanai N, Shimizu Y, Kariya S, Yasumatsu R, Yokota T, Fujii T, Tsukahara K, Yoshida M, Hanyu K, Ueda T, Hirakawa H, Takahashi S, Ono T, Sano D, Yamauchi M, Watanabe A, Omori K, Yamazaki T, Monden N, Kudo N, Arai M, Sakurai D, Asakage T, Doi I, Yamada T, Homma A

    International journal of clinical oncology   26 ( 5 )   1005 - 1006   2021.5   ISSN:1341-9625

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    Language:English  

    DOI: 10.1007/s10147-021-01879-y

    PubMed

  • A chromosome-scale strawberry genome assembly of a Japanese variety, Reikou

    Kenta Shirasawa, Hideki Hirakawa, Shinobu Nakayama, Shigemi Sasamoto, Hisano Tsuruoka, Chiharu Minami, Akiko Watanabe, Yoshie Kishida, Mitsuyo Kohara, Manabu Yamada, Tsunakazu Fujishiro, Akiko Komaki, Sachiko N Isobe

    2021.4

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    Publisher:Cold Spring Harbor Laboratory  

    <title>Abstract</title>Cultivated strawberry (<italic>Fragaria</italic> × <italic>ananassa</italic>) is an octoploid species (2n = 8x= 56) that is widely consumed around the world as both fresh and processed fruit. In this study, we report a chromosome-scale strawberry genome assembly of a Japanese variety, Reikou. The Illumina short reads derived from paired-end, mate-pair, and 10X Genomics libraries were assembled using Denovo MAGIC 3.0. The generated phased scaffolds consisted of 32,715 sequences with a total length of 1.4 Gb and an N50 length of 3.9 Mb. A total of 63 pseudomolecules including chr0 were created by aligning the scaffolds onto the Reikou S1 linkage maps with the IStraw90 Axiom SNP array and ddRAD-Seq. Meanwhile, genomes of diploid <italic>Fragaria</italic> species were resequenced and compared with the most similar chromosome-scale scaffolds to investigate the possible progenitor of each subgenome. Clustering analysis suggested that the most likely progenitors were <italic>F. vesca</italic> and <italic>F. iinumae</italic>. The phased pseudomolecules were assigned the scaffolds names with Av, Bi, and X, representing sequence similarity with <italic>F. vesca</italic> (Av), <italic>F. iinumae</italic> (Bi), and others (X), respectively. The result of a comparison with the Camerosa genome suggested the possibility of subgenome structure differences between the two varieties.

    DOI: 10.1101/2021.04.23.441065

  • Whole genome assembly in a Japanese strawberry cultivar, 'Reikou', and comparison with wild Fragaria genomes

    K. Shirasawa, C. Chung, D. Boncan, H. Hirakawa, F. Maeda, T. Wada, T. F. Chan, S. Isobe

    Acta Horticulturae   1309   175 - 179   2021.4   ISSN:0567-7572 eISSN:2406-6168

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    Publishing type:Research paper (scientific journal)  

    Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, which chromosome number is 2n=8x=56. In this study, we report a chromosome-scale strawberry genome assembly of a Japanese cultivar. Genomes of diploid Fragaria species were re-sequenced and compared with the most similar chromosome-scale scaffolds to investigate possible progenitor of each subgenomes. The Illumina short reads derived from paired-end, mate pair and 10X Genomics libraries were obtained from a Japanese cultivar, 'Reikou'. The scafffolds assembled using Denovo MAGIC 3.0 consisted of 32,715 sequences with a total length of 1.4 Gb and N50 length of 3.9 Mb. The scaffolds were aligned onto the 'Reikou' S1 linkage maps with IStraw90 Axiom SaNP array and ddRAD-Seq for pseudomolecule construction.

    DOI: 10.17660/ActaHortic.2021.1309.26

    Scopus

  • Comparative analysis using the draft genome sequence of California poppy (Eschscholzia californica) for exploring the candidate genes involved in benzylisoquinoline alkaloid biosynthesis International journal

    Yasuyuki Yamada, Hideki Hirakawa, Kentaro Hori, Yohei Minakuchi, Atsushi Toyoda, Nobukazu Shitan, Fumihiko Sato

    Bioscience, Biotechnology, and Biochemistry   85 ( 4 )   851 - 859   2021.3   ISSN:0916-8451 eISSN:1347-6947

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    <title>ABSTRACT</title>
    Genome characterization of California poppy (Eschscholzia californica cv. “Hitoezaki”), which produces pharmaceutically important benzylisoquinoline alkaloids (BIAs), was carried out using the draft genome sequence. The numbers of tRNA and rRNA genes were close to those of the other plant species tested, whereas the frequency of repetitive sequences was distinct from those species. Comparison of the predicted genes with those of Amborella trichopoda, Nelumbo nucifera, Solanum lycopersicum, and Arabidopsis thaliana, and analyses of gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway indicated that the enzyme genes involved in BIA biosynthesis were highly enriched in the California poppy genome. Further comparative analysis using the genome information of Papaver somniferum and Aquilegia coerulea, both BIA-producing plants, revealed that many genes encoding BIA biosynthetic enzymes, transcription factors, transporters, and candidate proteins, possibly related to BIA biosynthesis, were specifically distributed in these plant species.

    DOI: 10.1093/bbb/zbaa091

    PubMed

  • Whole-genome sequence analysis of mutations in rice plants regenerated from zygotes, mature embryos, and immature embryos

    Masako Ichikawa, Norio Kato, Erika Toda, Masakazu Kashihara, Yuji Ishida, Yukoh Hiei, Sachiko N. Isobe, Kenta Shirasawa, Hideki Hirakawa, Takashi Okamoto, Toshihiko Komari

    Breeding Science   2021.1   ISSN:1344-7610 eISSN:1347-3735

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    Publishing type:Research paper (scientific journal)   Publisher:Cold Spring Harbor Laboratory  

    <title>Abstract</title>Somaclonal variation was studied by whole-genome sequencing in rice plants (<italic>Oryza sativa</italic> L., ‘Nipponbare’) regenerated from the zygotes, mature embryos, and immature embryos of a single mother plant. The mother plant and its seed-propagated progeny were also sequenced. A total of 338 variants of the mother plant sequence were detected in the progeny, and mean values ranged from 9.0 of the seed-propagated plants to 37.4 of regenerants from mature embryos. The ratio of single nucleotide variants among the variants was 74.3%, and the natural mutation rate calculated using the variants in the seed-propagated plants was 1.2 × 10<sup>−8</sup>. The percentage and the mutation rate were consistent with the values reported previously. Plants regenerated from mature embryos had significantly more variants than different progeny types. Therefore, using zygotes and immature embryos can reduce somaclonal variation during the genetic manipulation of rice.

    DOI: 10.1101/2021.01.20.427397

  • Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype International journal

    Kenji Nashima, Kenta Shirasawa, Andrea Ghelfi, Hideki Hirakawa, Sachiko Isobe, Takuro Suyama, Takuya Wada, Takeshi Kurokura, Tatuya Uemachi, Mirai Azuma, Midori Akutsu, Masaharu Kodama, Yoshiko Nakazawa, Kiyoshi Namai

    DNA Research   28 ( 1 )   2021.1   ISSN:1340-2838 eISSN:1756-1663

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press (OUP)  

    <title>Abstract</title>
    Owing to its high ornamental value, the double flower phenotype of hydrangea (Hydrangea macrophylla) is one of its most important traits. In this study, genome sequence information was obtained to explore effective DNA markers and the causative genes for double flower production in hydrangea. Single-molecule real-time sequencing data followed by a Hi-C analysis were employed. Two haplotype-phased sequences were obtained from the heterozygous genome of hydrangea. One assembly consisted of 3,779 scaffolds (2.256 Gb in length and N50 of 1.5 Mb), the other also contained 3,779 scaffolds (2.227 Gb in length, and N50 of 1.4 Mb). A total of 36,930 genes were predicted in the sequences, of which 32,205 and 32,222 were found in each haplotype. A pair of 18 pseudomolecules was constructed along with a high-density single-nucleotide polymorphism (SNP) genetic linkage map. Using the genome sequence data, and two F2 populations, the SNPs linked to double flower loci (djo and dsu) were discovered. DNA markers linked to djo and dsu were developed, and these could distinguish the recessive double flower allele for each locus, respectively. The LEAFY gene is a very likely candidate as the causative gene for dsu, since frameshift was specifically observed in the double flower accession with dsu.

    DOI: 10.1093/dnares/dsaa026

    PubMed

    Other Link: http://academic.oup.com/dnaresearch/article-pdf/28/1/dsaa026/36170800/dsaa026.pdf

  • Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. International journal

    Amit Rai, Hideki Hirakawa, Ryo Nakabayashi, Shinji Kikuchi, Koki Hayashi, Megha Rai, Hiroshi Tsugawa, Taiki Nakaya, Tetsuya Mori, Hideki Nagasaki, Runa Fukushi, Yoko Kusuya, Hiroki Takahashi, Hiroshi Uchiyama, Atsushi Toyoda, Shoko Hikosaka, Eiji Goto, Kazuki Saito, Mami Yamazaki

    Nature communications   12 ( 1 )   405 - 405   2021.1

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    Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes' evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.

    DOI: 10.1038/s41467-020-20508-2

    PubMed

  • Identification of flavonoid 8-hydroxylase with gossypetin synthase activity from flower specific EST data of Lotus Japonicus.

    Yasuhide Hiraga, Norimoto Shimada, Yoshiki Nagashima, Kunihiro Suda, Tina Kanamori, Kanako Ishiguro, Yuka Sato, Hideki Hirakawa, Shusei Sato, Tomoyoshi Akashi, Yoshikazu Tanaka, Daisaku Ohta, Koh Aoki, Daisuke Shibata, Hideyuki Suzuki, Kota Kera

    Plant & cell physiology   62 ( 3 )   411 - 423   2021.1   ISSN:0032-0781

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    Lotus japonicus is a model legume, that accumulates 8-hydroxyflavonol derivatives such as gossypetin (8-hydroxyquercetin) 3-O-glycoside, which confer the yellow color to its petals. An enzyme, flavonoid 8-hydroxylase (LjF8H), is assumed to be involved in the biosynthesis, but the specific gene is yet to be identified. The LjF8H cDNA was isolated as an FAD-binding monooxygenase-like protein using flower buds and flower specific EST data of L. japonicus. LjF8H is a single copy gene on chromosome III consisting of six exons. The conserved FAD- and NAD(P)H-dependent oxidase motifs were found in LjF8H. Phylogenetic analysis suggested that LjF8H is a member of the flavin monooxygenase group, but distinctly different from other known flavonoid oxygenases. Analysis of recombinant yeast microsome expressing LjF8H revealed that the enzyme catalyzed the 8-hydroxylation of quercetin. Other flavonoids, such as naringenin, eriodictyol, apigenin, luteolin, taxifolin, and kaempferol also acted as substrates of LjF8H. This broad substrate acceptance was unlike known F8Hs in other plants. Interestingly, flavanone and flavanonol, which have saturated C-C bond at positions 2 and 3 of the flavonoid C-ring, produced 6-hyroxylflavonoids as a by-product of the enzymatic reaction. Furthermore, LjF8H only accepted the 2S-isomer of naringenin, suggesting the conformational state of the substrates might affect product specificity. The overexpression of LjF8H in Arabidopsis thaliana and Petunia hybrida synthesized gossypetin and 8-hydroxykaempferol, respectively, indicating that LjF8H was functional in plant cells. In conclusion, this study represents the first instance of cloning and identification of F8Hs responsible for gossypetin biosynthesis.

    DOI: 10.1093/pcp/pcaa171

    PubMed

  • Chromosome-level <i>de novo</i> genome assemblies of over 100 plant species

    Shirasawa Kenta, Harada Daijiro, Hirakawa Hideki, Isobe Sachiko, Kole Chittaranjan

    Breeding Science   71 ( 2 )   117 - 124   2021   ISSN:13447610 eISSN:13473735

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Japanese Society of Breeding  

    <p>Genome sequence analysis in higher plants began with the whole-genome sequencing of <i>Arabidopsis thaliana</i>. Owing to the great advances in sequencing technologies, also known as next-generation sequencing (NGS) technologies, genomes of more than 400 plant species have been sequenced to date. Long-read sequencing technologies, together with sequence scaffolding methods, have enabled the synthesis of chromosome-level <i>de novo</i> genome sequence assemblies, which has further allowed comparative analysis of the structural features of multiple plant genomes, thus elucidating the evolutionary history of plants. However, the quality of the assembled chromosome-level sequences varies among plant species. In this review, we summarize the status of chromosome-level assemblies of 114 plant species, with genome sizes ranging from 125 Mb to 16.9 Gb. While the average genome coverage of the assembled sequences reached up to 89.1%, the average coverage of chromosome-level pseudomolecules was 73.3%. Thus, further improvements in sequencing technologies and scaffolding, and data analysis methods, are required to establish gap-free telomere-to-telomere genome sequence assemblies. With the forthcoming new technologies, we are going to enter into a new genomics era where pan-genomics and the >1,000 or >1 million genomes’ project will be routine in higher plants.</p>

    DOI: 10.1270/jsbbs.20146

    PubMed

    CiNii Research

  • DNA marker for resistance to <i>Puccinia horiana</i> in chrysanthemum (<i>Chrysanthemum morifolium</i> Ramat.) “Southern Pegasus”

    Sumitomo Katsuhiko, Shirasawa Kenta, Isobe Sachiko N., Hirakawa Hideki, Harata Akiho, Kawabe Masato, Yagi Masafumi, Osaka Masaaki, Kunihisa Miyuki, Taniguchi Fumiya

    Breeding Science   71 ( 2 )   261 - 267   2021   ISSN:13447610 eISSN:13473735

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Japanese Society of Breeding  

    <p>White rust caused by <i>Puccinia horiana</i> Henn. adversely affects chrysanthemum (<i>Chrysanthemum morifolium</i> Ramat.) production. The breeding of resistant varieties is effective in controlling the disease. Here we aimed to develop DNA markers for the strong resistance to <i>P. horiana</i>. We conducted a linkage analysis based on the genome-wide association study (GWAS) method. We employed a biparental population for the GWAS, wherein the single nucleotide polymorphism (SNP) allele frequency could be predicted. The population was derived from crosses between a strong resistant “Southern Pegasus” and a susceptible line. The GWAS used simplex and double-simplex SNP markers selected out of SNP candidates mined from ddRAD-Seq data of an F<sub>1</sub> biparental population. These F<sub>1</sub> individuals segregated in a 1:1 ratio of resistant to susceptible. Twenty-one simplex SNPs were significantly associated with <i>P. horiana</i> resistance in “Southern Pegasus” and generated one linkage group. These results show the presence of a single resistance gene in “Southern Pegasus”. We identified the nearest SNP marker located 2.2 cM from <i>P. horiana</i> resistance locus and demonstrated this SNP marker-resistance link using an independent population. This is the first report of an effective DNA marker linked to a gene for <i>P. horiana</i> resistance in chrysanthemum.</p>

    DOI: 10.1270/jsbbs.20063

    PubMed

    CiNii Research

  • Root-knot nematode genetic diversity associated with host compatibility to sweetpotato cultivars. International journal

    Erika Asamizu, Kenta Shirasawa, Hideki Hirakawa, Hideaki Iwahori

    Molecular plant pathology   21 ( 8 )   1088 - 1098   2020.8   ISSN:1464-6722

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    Plant parasitic root-knot nematodes (RKN) such as Meloidogyne incognita cause significant crop losses worldwide. Although RKN are polyphagous, with wide host ranges, races with differing host compatibilities have evolved. Associations between genotype and infection phenotype in M. incognita have not yet been discovered. In this study, 48 M. incognita isolates were collected from geographically diverse fields in Japan and their genomes sequenced. The isolates exhibited various infection compatibilities to five sweetpotato (SP) cultivars and were assigned to SP races. Genome-wide association analysis identified 743 SNPs affecting gene coding sequences, a large number of which (575) were located on a single 1 Mb region. To examine how this polymorphic region evolved, nucleotide diversity (Pi) was scanned at the whole genome scale. The SNP-rich 1 Mb region exhibited high Pi values and was clearly associated with the SP races. SP1 and 2 races showed high Pi values in this region whereas the Pi values of SP3, 4, and 6 were low. Principal component analysis of isolates from this study and globally collected isolates showed selective divergence in this 1 Mb region. Our results suggest for the first time that the host could be a key determining factor stimulating the genomic divergence of M. incognita.

    DOI: 10.1111/mpp.12961

    PubMed

  • Effect of light on carotenoid and lipid production in the oleaginous yeast Rhodosporidium toruloides. International journal

    Khanh Dung Pham, Yosuke Shida, Atsushi Miyata, Takeru Takamizawa, Yoshiyuki Suzuki, Satoshi Ara, Harutake Yamazaki, Kazuo Masaki, Kazuki Mori, Sachiyo Aburatani, Hideki Hirakawa, Kosuke Tashiro, Satoru Kuhara, Hiroaki Takaku, Wataru Ogasawara

    Bioscience, biotechnology, and biochemistry   84 ( 7 )   1501 - 1512   2020.7   ISSN:0916-8451

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    The oleaginous yeast Rhodosporodium toruloides is receiving widespread attention as an alternative energy source for biofuels due to its unicellular nature, high growth rate and because it can be fermented on a large-scale. In this study, R. toruloides was cultured under both light and dark conditions in order to understand the light response involved in lipid and carotenoid biosynthesis. Our results from phenotype and gene expression analysis showed that R. toruloides responded to light by producing darker pigmentation with an associated increase in carotenoid production. Whilst there was no observable difference in lipid production, slight changes in the fatty acid composition were recorded. Furthermore, a two-step response was found in three genes (GGPSI, CAR1, and CAR2) under light conditions and the expression of the gene encoding the photoreceptor CRY1 was similarly affected.

    DOI: 10.1080/09168451.2020.1740581

    PubMed

  • Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale Lotus japonicus Gifu genome sequence. International journal

    Nadia Kamal, Terry Mun, Dugald Reid, Jie-Shun Lin, Turgut Yigit Akyol, Niels Sandal, Torben Asp, Hideki Hirakawa, Jens Stougaard, Klaus F X Mayer, Shusei Sato, Stig Uggerhøj Andersen

    DNA research : an international journal for rapid publication of reports on genes and genomes   27 ( 3 )   2020.6   ISSN:1340-2838

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    Lotus japonicus is a herbaceous perennial legume that has been used extensively as a genetically tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixation. Our aim is to improve the L. japonicus reference genome sequence, which has so far been based on Sanger and Illumina sequencing reads from the L. japonicus accession MG-20 and contained a large fraction of unanchored contigs. Here, we use long PacBio reads from L. japonicus Gifu combined with Hi-C data and new high-density genetic maps to generate a high-quality chromosome-scale reference genome assembly for L. japonicus. The assembly comprises 554 megabases of which 549 were assigned to six pseudomolecules that appear complete with telomeric repeats at their extremes and large centromeric regions with low gene density. The new L. japonicus Gifu reference genome and associated expression data represent valuable resources for legume functional and comparative genomics. Here, we provide a first example by showing that the symbiotic islands recently described in Medicago truncatula do not appear to be conserved in L. japonicus.

    DOI: 10.1093/dnares/dsaa015

    PubMed

  • The Ficus erecta genome aids Ceratocystis canker resistance breeding in common fig (F. carica). International journal

    Kenta Shirasawa, Hiroshi Yakushiji, Ryotaro Nishimura, Takeshige Morita, Shota Jikumaru, Hidetoshi Ikegami, Atsushi Toyoda, Hideki Hirakawa, Sachiko Isobe

    The Plant journal : for cell and molecular biology   102 ( 6 )   1313 - 1322   2020.6   ISSN:0960-7412

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    Ficus erecta, a wild relative of the common fig (F. carica), is a donor of Ceratocystis canker resistance in fig breeding programmes. Interspecific hybridization followed by recurrent backcrossing is an effective method to transfer the resistance trait from wild to cultivated fig. However, this process is time consuming and labour intensive for trees, especially for gynodioecious plants such as fig. In this study, genome resources were developed for F. erecta to facilitate fig breeding programmes. The genome sequence of F. erecta was determined using single-molecule real-time sequencing technology. The resultant assembly spanned 331.6 Mb with 538 contigs and an N50 length of 1.9 Mb, from which 51 806 high-confidence genes were predicted. Pseudomolecule sequences corresponding to the chromosomes of F. erecta were established with a genetic map based on single nucleotide polymorphisms from double-digest restriction-site-associated DNA sequencing. Subsequent linkage analysis and whole-genome resequencing identified a candidate gene for the Ceratocystis canker resistance trait. Genome-wide genotyping analysis enabled the selection of female lines that possessed resistance and effective elimination of the donor genome from the progeny. The genome resources provided in this study will accelerate and enhance disease-resistance breeding programmes in fig.

    DOI: 10.1111/tpj.14703

    PubMed

  • Identification of a novel major locus for resistance to pine wood nematode in <i>Pinus thunbergii</i>

    Hirao Tomonori, Matsunaga Koji, Hirakawa Hideki, Shirasawa Kenta, Isoda Keiya, Mishima Kentaro, Tamura Miho, Watanabe Atsushi

    The Japanese Forest Society Congress   131 ( 0 )   760   2020.5

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    Language:Japanese   Publisher:THE JAPANESE FORESTRY SOCIETY  

    <p>[in Japanese]</p>

    DOI: 10.11519/jfsc.131.0_760

    CiNii Research

  • AnAms1.0: A high-quality chromosome-scale assembly of a domestic cat Felis catus of American Shorthair breed

    Sachiko Isobe, Yuki Matsumoto, Claire Chung, Mika Sakamoto, Ting-Fung Chan, Hideki Hirakawa, Genki Ishihara, Hon-Ming Lam, Shinobu Nakayama, Shigemi Sasamoto, Yasuhiro Tanizawa, Akiko Watanabe, Kei Watanabe, Masaru Yagura, Yasukazu Nakamura

    bioRxiv   2020.5

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    Publisher:Cold Spring Harbor Laboratory  

    <title>Abstract</title>The domestic cat (<italic>Felis catus</italic>) is one of the most popular companion animals in the world. Comprehensive genomic resources will aid the development and application of veterinary medicine including to improve feline health, in particular, to enable precision medicine which is promising in human application. However, currently available cat genome assemblies were mostly built based on the Abyssinian cat breed which is highly inbred and has limited power in representing the vast diversity of the cat population. Moreover, the current reference assembly remains fragmented with sequences contained in thousands of scaffolds. We constructed a reference-grade chromosome-scale genome assembly of a domestic cat, <italic>Felis catus</italic> genome of American Shorthair breed, Anicom American shorthair 1.0 (AnAms1.0) with high contiguity (scaffold N50 &gt; 120 Mb), by combining multiple advanced genomic technologies, including PacBio long-read sequencing as well as sequence scaffolding by long-range genomic information obtained from Hi-C and optical mapping data. Homology-based and <italic>ab initio</italic> gene annotation was performed with the Iso-Seq data. Analyzed data is be publicly accessible on Cats genome informatics (Cats-I, <ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://cat.annotation.jp/">https://cat.annotation.jp/</ext-link>), a cat genome database established as a platform to facilitate the accumulation and sharing of genomic resources to improve veterinary care.

    DOI: 10.1101/2020.05.19.103788

  • Correction: The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants. International journal

    Takashi Akagi, Kenta Shirasawa, Hideki Nagasaki, Hideki Hirakawa, Ryutaro Tao, Luca Comai, Isabelle M Henry

    PLoS genetics   16 ( 5 )   e1008845   2020.5

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    [This corrects the article DOI: 10.1371/journal.pgen.1008566.].

    DOI: 10.1371/journal.pgen.1008845

    PubMed

  • Genome sequence and analysis of a Japanese radish (Raphanus sativus) cultivar named 'Sakurajima Daikon' possessing giant root. International journal

    Kenta Shirasawa, Hideki Hirakawa, Nobuko Fukino, Hiroyasu Kitashiba, Sachiko Isobe

    DNA research : an international journal for rapid publication of reports on genes and genomes   27 ( 2 )   2020.4   ISSN:1340-2838

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    AIM: The complex genome of a Japanese radish (Raphanus sativus) cultivar named 'Okute-Sakurajima' with an extremely large edible round root was analysed to explore its genomic characteristics. METHODS AND RESULTS: Single-molecule real-time technology was used to obtain long sequence reads to cover 60× of the genome. De novo assembly generated 504.5 Mb contigs consisting of 1,437 sequences with the N50 value of 1.2 Mb and included 94.1% of the core eukaryotic genes. Nine pseudomolecules, comprising 69.3% of the assembled contigs, were generated along with a high-density SNP genetic map. The sequence data thus established revealed the presence of structural variations and rearrangements in the Brassicaceae genomes. CONCLUSION AND PERSPECTIVE: A total of 89,915 genes were identified in the 'Okute-Sakurajima' genome, 30,033 of which were newly found in this study. The genome information reported here will not only contribute to the establishment of a new resource for the radish genomics but also provide insights into the molecular mechanisms underlying formation of the giant root.

    DOI: 10.1093/dnares/dsaa010

    PubMed

  • Comparative Genomic Analysis of Closely Related Acetobacter pasteurianus Strains Provides Evidence of Horizontal Gene Transfer and Reveals Factors Necessary for Thermotolerance. International journal

    Minenosuke Matsutani, Nami Matsumoto, Hideki Hirakawa, Yuh Shiwa, Hirofumi Yoshikawa, Akiko Okamoto-Kainuma, Morio Ishikawa, Naoya Kataoka, Toshiharu Yakushi, Kazunobu Matsushita

    Journal of bacteriology   202 ( 8 )   2020.3   ISSN:0021-9193

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    Acetobacter pasteurianus is an industrial strain used for the vinegar production. Many A. pasteurianus strains with different phenotypic characteristics have been isolated so far. To understand the genetic background underpinning these phenotypes, a comparative genomic analysis of A. pasteurianus strains was conducted. Based on bioinformatics and experimental results, we report the following. (i) The gene repertoire related to the respiratory chains showed that several horizontal gene transfer events occurred after the divergence of these strains, indicating that the respiratory chain in A. pasteurianus has the diversity to adapt to its environment. (ii) There is a clear difference in thermotolerance even between 12 closely related strains. NBRC 3279, NBRC 3284, and NBRC 3283, in particular, which have only 55 mutations in total, showed differences in thermotolerance. The Na+/H+ antiporter gene nhaK2 was mutated in the thermosensitive NBRC 3279 and NBRC 3284 strains and not in the thermotolerant NBRC 3283 strain. The Na+/H+ antiporter activity of the three strains and expression of nhaK2 gene from NBRC 3283 in the two thermosensitive strains showed that these mutations are critical for thermotolerance. These results suggested that horizontal gene transfer events and several mutations have affected the phenotypes of these closely related strains.IMPORTANCEAcetobacter pasteurianus, an industrial vinegar-producing strain, exhibits diverse phenotypic differences such as respiratory activity related to acetic acid production, acetic acid resistance, or thermotolerance. In this study, we investigated the correlations between genome sequences and phenotypes among closely related A. pasteurianus strains. The gene repertoire related to the respiratory chains showed that the respiratory components of A. pasteurianus has a diversity caused by several horizontal gene transfers and mutations. In three closely related strains with clear differences in their thermotolerances, we found that the insertion or deletion that occurred in the Na+/H+ antiporter gene nhaK2 is directly related to their thermotolerance. Our study suggests that a relatively quick mutation has occurred in the closely related A. pasteurianus due to its genetic instability and that this has largely affected its phenotype.

    DOI: 10.1128/JB.00553-19

    PubMed

  • Construction of a framework linkage map and genetic dissection of drought- and yield-related QTLs in horsegram (Macrotyloma uniflorum)

    Rakesh Kumar Chahota, Vikas Sharma, Maneet Rana, Reecha Sharma, Sunny Choudhary, T. R. Sharma, Kenta Shirasawa, Hideki Hirakawa, Sachiko N. Isobe

    EUPHYTICA   216 ( 4 )   2020.3   ISSN:0014-2336 eISSN:1573-5060

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    Horsegram (Macrotyloma uniflorum) is a legume species that is widely distributed throughout the Indian subcontinent. It is considered to be an important dietary protein supplement and nutraceutical. Horsegram has a great potential for fulfilling future pulse crop demand due to its inherent ability to grow under very low moisture conditions. However, the genome structure and organization of this crop is poorly understood, thereby limiting the effective use of gene resources for genetic improvement. We report here our construction of the first framework linkage map of horsegram, consisting of 211 molecular markers (157 SSR, 39 RAPD, 8 ISSR and 7 COS), using a mapping population of 190 recombinant inbred lines derived from a cross between parental lines HPK4 and HPKM249. The map comprises 13 linkage groups (LGs) that span 1423.4 cM, with a mean marker interval of 9.6 cM. Phenotypic data for eight agronomic traits were recorded for 2 years and utilized to detect associated quantitative trait loci (QTLs). Five QTLs for four traits related to drought (days to temporary wilting, root length) and yield (numbers of seeds per plant, days to maturity) were detected on five LGs, with an LOD threshold of 4.0. The linkage and QTL analysis reported here provides useful information for future research work pertaining to the construction of highly enriched genetic maps as well as to the development of drought-resistant and high-yielding varieties of horsegram using marker-assisted selection.

    DOI: 10.1007/s10681-020-02583-0

    Web of Science

  • The Lotus japonicus nucleoporin GLE1 is involved in symbiotic association with rhizobia. International journal

    Akito Imai, Mai Ohtani, Asami Nara, Anna Tsukakoshi, Aya Narita, Hideki Hirakawa, Shusei Sato, Norio Suganuma

    Physiologia plantarum   168 ( 3 )   590 - 600   2020.3   ISSN:0031-9317

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    Nucleoporins are components of the nuclear pore complexes, channels that regulate the transport of macromolecules between the nucleus and cytoplasm. The nucleoporin GLE1 (GLFG lethal1) functions in the export of messenger RNAs containing poly(A) tails from the nucleus into the cytoplasm. Here we investigated a mutant of the model legume Lotus japonicus that was defective in GLE1, which we designated Ljgle1. The growth of Ljgle1 was retarded under symbiotic association with rhizobia, and the nitrogen-fixation activities of the nodules were around one-third of those in the wild-type plant. The growth of Ljgle1 was not substantialy recovered by supplemention of combined nitrogen. Nodules formed on the Ljgle1 were smaller than those on the wild-type and colored faint pink. The numbers of infected cells of nodules on the Ljgle1 were smaller than on the wild-type plant, and the former cells remained undeveloped. Rhizobia in the cells of the Ljgle1 exhibited disordered forms, and the symbiosome membrane was closely attached to the bacterial membrane. These results indicate that GLE1 plays a distinct role in the symbiotic association between legumes and rhizobia.

    DOI: 10.1111/ppl.12996

    PubMed

  • The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants International journal

    Akagi Takashi, Shirasawa Kenta, Nagasaki Hideki, Hirakawa Hideki, Tao Ryutaro, Comai Luca, Henry Isabelle M.

    PLOS Genetics   16 ( 2 )   e1008566   2020.2   ISSN:15537404 eISSN:15537404

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    Most angiosperms bear hermaphroditic flowers, but a few species have evolved outcrossing strategies, such as dioecy, the presence of separate male and female individuals. We previously investigated the mechanisms underlying dioecy in diploid persimmon (D. lotus) and found that male flowers are specified by repression of the autosomal gene MeGI by its paralog, the Y-encoded pseudo-gene OGI. This mechanism is thought to be lineage-specific, but its evolutionary path remains unknown. Here, we developed a full draft of the diploid persimmon genome (D. lotus), which revealed a lineage-specific whole-genome duplication event and provided information on the architecture of the Y chromosome. We also identified three paralogs, MeGI, OGI and newly identified Sister of MeGI (SiMeGI). Evolutionary analysis suggested that MeGI underwent adaptive evolution after the whole-genome duplication event. Transformation of tobacco plants with MeGI and SiMeGI revealed that MeGI specifically acquired a new function as a repressor of male organ development, while SiMeGI presumably maintained the original function. Later, a segmental duplication event spawned MeGI’s regulator OGI on the Y-chromosome, completing the path leading to dioecy, and probably initiating the formation of the Y-chromosome. These findings exemplify how duplication events can provide flexible genetic material available to help respond to varying environments and provide interesting parallels for our understanding of the mechanisms underlying the transition into dieocy in plants.

    DOI: 10.1371/journal.pgen.1008566

    PubMed

    CiNii Research

    Other Link: https://dx.plos.org/10.1371/journal.pgen.1008566

  • Identification of genome-wide single-nucleotide polymorphisms among geographically diverse radish accessions. International journal

    Hiroto Kobayashi, Kenta Shirasawa, Nobuko Fukino, Hideki Hirakawa, Takashi Akanuma, Hiroyasu Kitashiba

    DNA research : an international journal for rapid publication of reports on genes and genomes   27 ( 1 )   2020.2   ISSN:1340-2838

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    Radish (Raphanus sativus L.) is cultivated around the world as a vegetable crop and exhibits diverse morphological and physiological features. DNA polymorphisms are responsible for differences in traits among cultivars. In this study, we determined genome-wide single-nucleotide polymorphisms (SNPs) among geographically diverse radish accessions using the double-digest restriction site-associated DNA sequencing (ddRAD-Seq) method. A total of 52,559 SNPs was identified in a collection of over 500 radish accessions (cultivated and wild) from East Asia, South and Southeast Asia, and the Occident and Near East. In addition, 2,624 SNP sites without missing data (referred to as common SNP sites) were identified among 510 accessions. Genetic diversity analyses, based on the common SNP sites, divided the cultivated radish accessions into four main groups, each derived from four geographical areas (Japan, East Asia, South and Southeast Asia, and the Occident and Near East). Furthermore, we discuss the origin of cultivated radish and its migration from the West to East Asia. SNP data generated in this work will facilitate further genetic studies on the radish breeding and production of DNA markers.

    DOI: 10.1093/dnares/dsaa001

    PubMed

  • QTL analysis for flowering time in carnation (Dianthus caryophyllus L.)

    Masafumi Yagi, Kenta Shirasawa, Hideki Hirakawa, Sachiko Isobe, Junko Matsuno, Yuichi Uno, Koji Tanase, Takashi Onozaki, Hiroyasu Yamaguchi

    SCIENTIA HORTICULTURAE   262   2020.2   ISSN:0304-4238 eISSN:1879-1018

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:ELSEVIER  

    Flowering time is one of the most important traits in carnation (Dianthus caryophyllus L.) breeding because it decides the yearly yield. Two previously developed mapping populations were used to determine the number and effect of quantitative trait loci (QTLs) for flowering time. Flowering time showed large phenotypic segregation in two F-2 populations and in different years. Despite the different populations and different years, one major common QTL for flowering time was detected in linkage group 10 with the effect explaining from 18.2%-22.5% of the overall phenotypic variance. We developed a DNA marker, qD1Flw1-sc43-4, that was located close to the detected QTL for flowering time. We could distinguish the flowering time and categorize the genotypes of an F-1 population derived from a cross between late flowering 'Light Pink Barbara' and early flowering 'Kaneainou 1 go' using the qD1Flw1-sc43-4 marker. Our results suggest that flowering time in carnation involves several genetic factors. In this study, we identified one of the major factors for flowering time and developed a DNA marker that was tightly linked to the major QTL.

    DOI: 10.1016/j.scienta.2019.109053

    Web of Science

  • The rhizobial autotransporter determines the symbiotic nitrogen fixation activity of Lotus japonicus in a host-specific manner. International journal

    Yoshikazu Shimoda, Yuki Nishigaya, Hiroko Yamaya-Ito, Noritoshi Inagaki, Yosuke Umehara, Hideki Hirakawa, Shusei Sato, Toshimasa Yamazaki, Makoto Hayashi

    Proceedings of the National Academy of Sciences of the United States of America   117 ( 3 )   1806 - 1815   2020.1   ISSN:0027-8424

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    Leguminous plants establish endosymbiotic associations with rhizobia and form root nodules in which the rhizobia fix atmospheric nitrogen. The host plant and intracellular rhizobia strictly control this symbiotic nitrogen fixation. We recently reported a Lotus japonicus Fix- mutant, apn1 (aspartic peptidase nodule-induced 1), that impairs symbiotic nitrogen fixation. APN1 encodes a nodule-specific aspartic peptidase involved in the Fix- phenotype in a rhizobial strain-specific manner. This host-strain specificity implies that some molecular interactions between host plant APN1 and rhizobial factors are required, although the biological function of APN1 in nodules and the mechanisms governing the interactions are unknown. To clarify how rhizobial factors are involved in strain-specific nitrogen fixation, we explored transposon mutants of Mesorhizobium loti strain TONO, which normally form Fix- nodules on apn1 roots, and identified TONO mutants that formed Fix+ nodules on apn1 The identified causal gene encodes an autotransporter, part of a protein secretion system of Gram-negative bacteria. Expression of the autotransporter gene in M. loti strain MAFF3030399, which normally forms Fix+ nodules on apn1 roots, resulted in Fix- nodules. The autotransporter of TONO functions to secrete a part of its own protein (a passenger domain) into extracellular spaces, and the recombinant APN1 protein cleaved the passenger protein in vitro. The M. loti autotransporter showed the activity to induce the genes involved in nodule senescence in a dose-dependent manner. Therefore, we conclude that the nodule-specific aspartic peptidase, APN1, suppresses negative effects of the rhizobial autotransporter in order to maintain effective symbiotic nitrogen fixation in root nodules.

    DOI: 10.1073/pnas.1913349117

    PubMed

  • 3-1-42 農耕地利用の強度に応答したアーバスキュラー菌根菌群集の収斂と多様性の維持機構(3-1 土壌生物の生態と機能 2020年度岡山大会)

    丹羽 理恵子, 小八重 善裕, 大友 量, 林 正紀, 唐澤 敏彦, 神山 拓也, 丸山 隼人, 江沢 辰広, 佐藤 修正, 平川 英樹, 吉田 重信, 佐藤 孝, 鈴木 貴恵, 佐藤 匠, 俵谷 圭太郎, 福永 亜矢子

    日本土壌肥料学会講演要旨集   66   34 - 34   2020   ISSN:0288-5840

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    Language:Japanese   Publisher:一般社団法人 日本土壌肥料学会  

    DOI: 10.20710/dohikouen.66.0_34_3

  • Advances of Whole Genome Sequencing in Strawberry with NGS Technologies

    Isobe Sachiko, Shirasawa Kenta, Hirakawa Hideki

    The Horticulture Journal   89 ( 2 )   108 - 114   2020   ISSN:2189-0102

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    Language:English   Publisher:The Japanese Society for Horticultural Science  

    <p>Next generation sequencing (NGS) is one of the most impactful technologies to appear in the 21<sup>st</sup> century, and has already brought important changes to agriculture, especially in the field of breeding. Construction of a reference genome is key to the advancement of genomic studies, and therefore, <i>de novo</i> whole genome assembly has been performed in various plants, including strawberry. Strawberry (<i>Fragaria</i> × <i>ananassa</i>) is an allo-octoploid species (2<i>n</i> = 8<i>x</i> = 56), which has four discriminable subgenomes. Because of its complex genome structure, <i>de novo</i> whole genome assembly in strawberry has been considered a difficult challenge. However, recent advances of NGS technologies have allowed the construction of chromosome-scale <i>de novo</i> whole genome assembly. In this manuscript, we review the recent advances in <i>de novo</i> whole genome sequencing in strawberry and other <i>Fragaria</i> species. The genome structure and domestication history in strawberry is one of the largest questions in genetic and genomic studies in strawberry. Therefore, the domestication history in strawberry is also be reviewed based on comparisons of genes and genome sequences across <i>Fragaria</i> species.</p>

    DOI: 10.2503/hortj.UTD-R012

    CiNii Books

  • Genome assembly and analysis of <i>Lyophyllum shimeji</i>

    Kobayashi Y., Shibata T., Hirakawa H., Yamada A., Shigenobu S., Nishiyama T., Hasebe M., Kawaguchi M.

    Abstracts of Papers Presented at the Meeting of the Mycological Society of Japan   64 ( 0 )   65   2020

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    Language:Japanese   Publisher:The Mycological Society of Japan  

    DOI: 10.11556/msj7abst.64.0_65b

    CiNii Research

  • Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants. International journal

    Andrea Ghelfi, Kenta Shirasawa, Hideki Hirakawa, Sachiko Isobe

    Bioinformatics (Oxford, England)   35 ( 21 )   4427 - 4429   2019.11   ISSN:1367-4803

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    SUMMARY: Hayai-Annotation Plants is a browser-based interface for an ultra-fast and accurate functional gene annotation system for plant species using R. The pipeline combines the sequence-similarity searches, using USEARCH against UniProtKB (taxonomy Embryophyta), with a functional annotation step. Hayai-Annotation Plants provides five layers of annotation: i) protein name; ii) gene ontology terms consisting of its three main domains (Biological Process, Molecular Function and Cellular Component); iii) enzyme commission number; iv) protein existence level; and v) evidence type. It implements a new algorithm that gives priority to protein existence level to propagate GO and EC information and annotated Arabidopsis thaliana representative peptide sequences (Araport11) within 5 min at the PC level. AVAILABILITY AND IMPLEMENTATION: The software is implemented in R and runs on Macintosh and Linux systems. It is freely available at https://github.com/kdri-genomics/Hayai-Annotation-Plants under the GPLv3 license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

    DOI: 10.1093/bioinformatics/btz380

    PubMed

  • Current status in whole genome sequencing and analysis of Ipomoea spp. International journal

    Sachiko Isobe, Kenta Shirasawa, Hideki Hirakawa

    Plant cell reports   38 ( 11 )   1365 - 1371   2019.11   ISSN:0721-7714

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    The recent advances of next-generation sequencing have made it possible to construct reference genome sequences in divergent species. However, de novo assembly at the chromosome level remains challenging in polyploid species, due to the existence of more than two pairs of homoeologous chromosomes in one nucleus. Cultivated sweet potato (Ipomoea batatas (L.) Lam) is a hexaploid species with 90 chromosomes (2n = 6X = 90). Although the origin of sweet potato is also still under discussion, diploid relative species, I. trifida and I. triloba have been considered as one of the most possible progenitors. In this manuscript, we review the recent results and activities of whole-genome sequencing in the genus Ipomoea series Batatas, I. trifida, I. triloba and sweet potato (I. batatas). Most of the results of genome assembly suggest that the genomes of sweet potato consist of two pairs and four pairs of subgenomes, i.e., B1B1B2B2B2B2. The results also revealed the relation between sweet potato and other Ipomoea species. Together with the development of bioinformatics approaches, the large-scale publicly available genome and transcript sequence resources and international genome sequencing streams are expected to promote the genome sequence dissection in sweet potato.

    DOI: 10.1007/s00299-019-02464-4

    PubMed

  • Construction of genetic linkage map and identification of a novel major locus for resistance to pine wood nematode in Japanese black pine (Pinus thunbergii). International journal

    Tomonori Hirao, Koji Matsunaga, Hideki Hirakawa, Kenta Shirasawa, Keiya Isoda, Kentaro Mishima, Miho Tamura, Atsushi Watanabe

    BMC plant biology   19 ( 1 )   424 - 424   2019.10

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    BACKGROUND: Pine wilt disease (PWD), which is caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus, is currently the greatest threat to pine forests in Europe and East Asian countries including Japan. Constructing a detailed linkage map of DNA markers and identifying PWD resistance genes/loci lead to improved resistance in Pinus thunbergii, as well as other Pinus species that are also susceptible to PWD. RESULTS: A total F1 mapping population of 188 individuals derived from a cross between the PWD-resistant P. thunbergii varieties 'Tanabe 54' (resistant rank 2 to PWD) and 'Tosashimizu 63' (resistant rank 4 to PWD) was inoculated with PWN, and was evaluated for disease symptoms. To perform linkage analysis for PWN resistance, a set of three maps was constructed; two parental maps generated using the integrated two-way pseudo-testcross method, and a consensus map with population-type cross-pollination. The linkage map of 'Tanabe 54' consisted of 167 loci, and covered 14 linkage groups (LGs), with a total genetic distance of 1214.6 cM. The linkage map of 'Tosashimizu 63' consisted of 252 loci, and covered 14 LGs, with a total genetic distance of 1422.1 cM. The integrated consensus map comprised 12 LGs with the basic chromosome number of P. thunbergii, and a total genetic distance of 1403.6 cM. Results from quantitative trait loci (QTL) analysis using phenotype data and linkage maps indicated that PWN resistance is controlled by a single dominant allele, which was derived from the 'Tanabe 54' female parent. This major QTL was located on linkage group 3 and was designated PWD1 for PINE WILT DISEASE 1. CONCLUSIONS: The PWD1 locus is a major resistance QTL located on the Pinus consensus LG03 that acts in a dominant manner to confer pine wood nematode resistance. Information from the present study will be useful for P. thunbergii breeding programs to improve resistance to PWD, and also to help identify susceptibility genes in Pinus species.

    DOI: 10.1186/s12870-019-2045-y

    PubMed

  • 種を超えた植物ゲノム情報統合のためのデータリンク基盤の構築

    市原 寿子, 磯部 祥子, 平川 英樹, 原田 大士朗, ジェルフィ アンドレア, 小原 光代, 山田 学, 白澤 沙知子, 中村 保一, 田村 卓郎, 杉原 英志, 田畑 哲之, 中谷 明弘

    1   2019.10

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    Publisher:バイオサイエンスデータベースセンター  

    DOI: 10.18908/togo2019.p027

    CiNii Research

  • Phased genome sequence of an interspecific hybrid flowering cherry, 'Somei-Yoshino' (Cerasus × yedoensis). International journal

    Kenta Shirasawa, Tomoya Esumi, Hideki Hirakawa, Hideyuki Tanaka, Akihiro Itai, Andrea Ghelfi, Hideki Nagasaki, Sachiko Isobe

    DNA research : an international journal for rapid publication of reports on genes and genomes   26 ( 5 )   379 - 389   2019.10   ISSN:1340-2838

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    We report the phased genome sequence of an interspecific hybrid, the flowering cherry 'Somei-Yoshino' (Cerasus × yedoensis). The sequence data were obtained by single-molecule real-time sequencing technology, split into two subsets based on genome information of the two probable ancestors, and assembled to obtain two haplotype phased genome sequences of the interspecific hybrid. The resultant genome assembly consisting of the two haplotype sequences spanned 690.1 Mb with 4,552 contigs and an N50 length of 1.0 Mb. We predicted 95,076 high-confidence genes, including 94.9% of the core eukaryotic genes. Based on a high-density genetic map, we established a pair of eight pseudomolecule sequences, with highly conserved structures between the two haplotype sequences with 2.4 million sequence variants. A whole genome resequencing analysis of flowering cherries suggested that 'Somei-Yoshino' might be derived from a cross between C. spachiana and either C. speciosa or its relatives. A time-course transcriptome analysis of floral buds and flowers suggested comprehensive changes in gene expression in floral bud development towards flowering. These genome and transcriptome data are expected to provide insights into the evolution and cultivation of flowering cherry and the molecular mechanism underlying flowering.

    DOI: 10.1093/dnares/dsz016

    PubMed

  • A pure line derived from a self-compatible Chrysanthemum seticuspe mutant as a model strain in the genus Chrysanthemum. International journal

    Michiharu Nakano, Kenji Taniguchi, Yu Masuda, Toshiaki Kozuka, Yuki Aruga, Jin Han, Koichiro Motohara, Masashi Nakata, Katsuhiko Sumitomo, Tamotsu Hisamatsu, Yoshihiro Nakano, Masafumi Yagi, Hideki Hirakawa, Sachiko N Isobe, Kenta Shirasawa, Yumi Nagashima, Haiyan Na, Li Chen, Guolu Liang, Ruiyan Chen, Makoto Kusaba

    Plant science : an international journal of experimental plant biology   287   110174 - 110174   2019.10   ISSN:0168-9452

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    Asteraceae is the largest family of angiosperms, comprising approximately 24,000 species. Molecular genetic studies of Asteraceae are essential for understanding plant diversity. Chrysanthemum morifolium is the most industrially important ornamental species in Asteraceae. Most cultivars of C. morifolium are autohexaploid and self-incompatible. These properties are major obstacles to the genetic analysis and modern breeding of C. morifolium. Furthermore, high genome heterogeneity complicates molecular biological analyses. In this study, we developed a model strain in the genus Chrysanthemum. C. seticuspe is a diploid species with a similar flowering property and morphology to C. morifolium and can be subjected to Agrobacterium-mediated transformation. We isolated a natural self-compatible mutant of C. seticuspe and established a pure line through repeated selfing and selection. The resultant strain, named Gojo-0, was favorable for genetic analyses, including isolation of natural and induced mutants, and facilitated molecular biological analysis, including whole genome sequencing, owing to the simplicity and homogeneity of its genome. Interspecific hybridization with Chrysanthemum species was possible, enabling molecular genetic analysis of natural interspecific variations. The accumulation of research results and resources using Gojo-0 as a platform is expected to promote molecular genetic studies on the genus Chrysanthemum and the genetic improvement of chrysanthemum cultivars.

    DOI: 10.1016/j.plantsci.2019.110174

    PubMed

  • Genome-wide association study overcomes the genome complexity in autohexaploid chrysanthemum and tags SNP markers onto the flower color genes. International journal

    Katsuhiko Sumitomo, Kenta Shirasawa, Sachiko Isobe, Hideki Hirakawa, Tamotsu Hisamatsu, Yoshihiro Nakano, Masafumi Yagi, Akemi Ohmiya

    Scientific reports   9 ( 1 )   13947 - 13947   2019.9

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    The use of DNA markers has revolutionized selection in crop breeding by linkage mapping and QTL analysis, but major problems still remain for polyploid species where marker-assisted selection lags behind the situation in diploids because of its high genome complexity. To overcome the complex genetic mode in the polyploids, we investigated the development of a strategy of genome-wide association study (GWAS) using single-dose SNPs, which simplify the segregation patterns associated polyploids, with respect to the development of DNA markers. In addition, we employed biparental populations for the GWAS, wherein the SNP allele frequency could be predicted. The research investigated whether the method could be used to effectively develop DNA markers for petal color in autohexaploid chrysanthemum (Chrysanthemum morifolium; 2n = 6x = 54). The causal gene for this trait is already-known CmCCD4a encoding a dioxygenase which cleaves carotenoids in petals. We selected 9,219 single-dose SNPs, out of total 52,489 SNPs identified by dd-RAD-Seq, showing simplex (1 × 0) and double-simplex (1 × 1) inheritance pattern according to alternative allele frequency with respect to the SNP loci in the F1 population. GWAS, using these single-dose SNPs, discovered highly reproducible SNP markers tightly linked to the causal genes. This is the first report of a straightforward GWAS-based marker developing system for use in autohexaploid species.

    DOI: 10.1038/s41598-019-50028-z

    PubMed

  • P3-1-5 未利用地から農地への土地利用変化に伴う土壌微生物群集構造の変化(3-1 土壌生物の生態と機能,2019年静岡大会)

    高田 理江, 花野 滋, 宮本 託志, 滝澤 理仁, 冨永 達, 柴田 大輔, 櫻井 望, 平川 英樹, 小林 優

    日本土壌肥料学会講演要旨集   65   31 - 31   2019.9   ISSN:0288-5840 eISSN:2424-0575

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    Language:Japanese   Publisher:一般社団法人 日本土壌肥料学会  

    DOI: 10.20710/dohikouen.65.0_31_2

    CiNii Research

  • De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis International journal

    Hideki Hirakawa, Katsuhiko Sumitomo, Tamotsu Hisamatsu, Soichiro Nagano, Kenta Shirasawa, Yohei Higuchi, Makoto Kusaba, Masaji Koshioka, Yoshihiro Nakano, Masafumi Yagi, Hiroyasu Yamaguchi, Kenji Taniguchi, Michiharu Nakano, Sachiko N. Isobe

    DNA RESEARCH   26 ( 3 )   195 - 203   2019.6   ISSN:1340-2838 eISSN:1756-1663

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:OXFORD UNIV PRESS  

    Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n = 6x = 54) and large genome size. The diploid Chrysanthemum seticuspe is often used as a model of cultivated chrysanthemum, since the two species are closely related. To expand our knowledge of the cultivated chrysanthemum, we here performed de novo whole-genome assembly in C. seticuspe using the Illumina sequencing platform. XMRS10, a C. seticuspe accession developed by five generations of self-crossing from a self-compatible strain, AEV2, was used for genome sequencing. The 2.72 Gb of assembled sequences (CSE_r1.0), consisting of 354,212 scaffolds, covered 89.0% of the 3.06 Gb C. seticuspe genome estimated by k-mer analysis. The N50 length of scaffolds was 44,741 bp. For protein-encoding genes, 71,057 annotated genes were deduced (CSE_r1.1_cds). Next, based on the assembled genome sequences, we performed linkage map construction, gene discovery and comparative analyses for C. seticuspe and cultivated chrysanthemum. The generated C. seticuspe linkage map revealed skewed regions in segregation on the AEV2 genome. In gene discovery analysis, candidate flowering-related genes were newly found in CSE_r1.1_cds. Moreover, single nucleotide polymorphism identification and annotation on the C. x morifolium genome showed that the C. seticuspe genome was applicable to genetic analysis in cultivated chrysanthemums. The genome sequences assembled herein are expected to contribute to future chrysanthemum studies. In addition, our approach demonstrated the usefulness of short-read genome assembly and the importance of choosing an appropriate next genome sequencing technology based on the purpose of the post-genome analysis.

    DOI: 10.1093/dnares/dsy048

    Web of Science

    PubMed

  • Transcriptome analysis of the Japanese cedar clones after gibberellin treatment

    Tsubomura Miyoko, Mishima Kentaro, Hirao Tomonori, Nagano Soichiro, Hirakawa Hideki

    The Japanese Forest Society Congress   130 ( 0 )   579   2019.5

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    Language:Japanese   Publisher:THE JAPANESE FORESTRY SOCIETY  

    <p>[in Japanese]</p>

    DOI: 10.11519/jfsc.130.0_579

    CiNii Research

  • Widely targeted metabolome and transcriptome landscapes of Allium fistulosum-A. cepa chromosome addition lines revealed a flavonoid hot spot on chromosome 5A. Reviewed International journal

    Mostafa Abdelrahman, Sho Hirata, Yuji Sawada, Masami Yokota Hirai, Shusei Sato, Hideki Hirakawa, Yoko Mine, Keisuke Tanaka, Masayoshi Shigyo

    Scientific reports   9 ( 1 )   3541 - 3541   2019.3

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    Here, we report a comprehensive analysis of the widely targeted metabolome and transcriptome profiles of Allium fistulosum L. (FF) with the single extra chromosome of shallot [A. cepa L. Aggregatum group (AA)] to clarify the novel gene functions in flavonoid biosynthesis. An exhaustive metabolome analysis was performed using the selected reaction monitoring mode of liquid chromatography-tandem quadrupole mass spectrometry, revealing a specific accumulation of quercetin, anthocyanin and flavone glucosides in AA and FF5A. The addition of chromosome 5A from the shallot to A. fistulosum induced flavonoid accumulation in the recipient species, which was associated with the upregulation of several genes including the dihydroflavonol 4-reductase, chalcone synthase, flavanone 3-hydroxylase, UDP-glucose flavonoid-3-O-glucosyltransferase, anthocyanin 5-aromatic acyltransferase-like, pleiotropic drug resistance-like ATP binding cassette transporter, and MYB14 transcriptional factor. Additionally, an open access Allium Transcript Database (Allium TDB, http://alliumtdb.kazusa.or.jp ) was generated by using RNA-Seq data from different genetic stocks including the A. fistulosum-A. cepa monosomic addition lines. The functional genomic approach presented here provides an innovative means of targeting the gene responsible for flavonoid biosynthesis in A. cepa. The understanding of flavonoid compounds and biosynthesis-related genes would facilitate the development of noble Allium varieties with unique chemical constituents and, subsequently, improved plant stress tolerance and human health benefits.

    DOI: 10.1038/s41598-019-39856-1

    PubMed

  • Diversity of NADH dehydrogenases in acetic acid bacteria: adaptation to modify their phenotype through gene expansions and losses and neo-functionalization International journal

    Minenosuke Matsutani, Hideki Hirakawa, Feronika Heppy Sriherfyna, Toshiharu Yakushi, Kazunobu Matsushita

    MICROBIOLOGY-SGM   165 ( 3 )   287 - 291   2019.3   ISSN:1350-0872 eISSN:1465-2080

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    NADH dehydrogenase plays an important role in the central metabolism of almost all organisms, including acetic acid bacteria (AAB). In this study, the gene diversity of the NADH dehydrogenases in AAB was investigated. The distribution of the genes of the type I and type II NADH dehydrogenases in AAB was mostly congruent with their phylogenetic relationships. There are two phylogenetically distinct type I NADH dehydrogenase complexes, complex IA and complex IE. Complex IA', which lacks the nuoM gene from complex IA, was only conserved in the genera Acetobacter, Gluconacetobacter and Komagataeibacter, which all have the ability to perform acetic acid fermentation, whereas the complex IE gene cluster was found randomly in several species of AAB. Almost all AAB, excluding the early-diverged species, had the type II NADH dehydrogenase, while some of the species also had the homologue with an amino acid replacement at the residue responsible for NADPH oxidation ability. Thus, the gene repertoire of NADH dehydrogenases shows a history of adaptation towards their habitats through gene expansions and losses and neo-functionalization in AAB.

    DOI: 10.1099/mic.0.000774

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  • Identification of potential genes involved in triterpenoid saponins biosynthesis in Gleditsia sinensis by transcriptome and metabolome analyses.

    Yusuke Kuwahara, Daisuke Nakajima, Sayaka Shinpo, Michimi Nakamura, Noriaki Kawano, Nobuo Kawahara, Mami Yamazaki, Kazuki Saito, Hideyuki Suzuki, Hideki Hirakawa

    Journal of natural medicines   73 ( 2 )   369 - 380   2019.3   ISSN:1340-3443

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    Gleditsia sinensis is widely used as a medicinal plant in Asia, especially in China. Triterpenes, alkaloids, and sterols were isolated from Gleditsia species. Among them, triterpenoid saponins are very important metabolites owing to their various pharmacological activities. However, the triterpenoid saponin biosynthesis pathway has not been well characterized. In the present study, we performed de novo transcriptome assembly for 14.3 Gbps of clean reads sequenced from nine tissues of G. sinensis. The results showed that 81,511 unique transcripts (unitranscripts) (47,855 unigenes) were constructed, of which 31,717 unigenes were annotated with Gene Ontology and EC numbers by Blast2GO against the NCBI-nr protein database. We also analyzed the metabolite contents in the same nine tissues by LS-MS/MS, and saponins including gleditsioside I were found in fruit at higher levels. Many of the genes with tissue-specific expression in fruit are involved in the flavonoid biosynthesis pathway, and many of those have UDP-glucosyltransferase (UGT) activity. We constructed a saponin biosynthesis pathway and identified two key enzyme families in the triterpenoid saponin biosynthesis pathway, cytochrome P450 and UDP-glucosyltransferase, that are encoded by 37 unigenes and 77 unigenes, respectively. CYP72A, CYP716A, and CYP88D, which are known as key enzymes for saponin biosynthesis, were also identified among the P450s. Our results provide insight into the secondary metabolite biosynthesis and serve as important resources for future research and cultivation of G. sinensis.

    DOI: 10.1007/s11418-018-1270-2

    PubMed

  • Structual analysis of candidate genes for sex-determination in the genus <i>Spinacia</i>

    Okazaki Y, Hirakawa H, Onodera Y

    Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan   60 ( 0 )   74 - 75   2019   ISSN:2432-0307 eISSN:24320307

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    Language:Japanese   Publisher:Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  

    DOI: 10.20751/hdanwakai.60.0_74

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    J-GLOBAL

  • Molecular evidence for recent divergence of X- and Y-linked gene pairs in Spinacia oleracea L. International journal

    Yosuke Okazaki, Satoshi Takahata, Hideki Hirakawa, Yutaka Suzuki, Yasuyuki Onodera

    PloS one   14 ( 4 )   e0214949   2019

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    Dioecy has evolved recently and independently from cosexual populations in many angiosperm lineages, providing opportunities to understand the evolutionary process underlying this transition. Spinach (Spinacia oleracea) is a dioecious plant with homomorphic sex chromosomes (XY). Although most of the spinach Y chromosome recombines with the X chromosome, a region around the male-determining locus on Y does not recombine with its X counterpart, suggesting that this region might be related to the evolution of dioecy in the species. To identify genes located in the non-recombining region (MSY, male-specific region of Y), RNA-seq analysis of male and female progeny plants (eight each) from a sib-cross of a dioecious line was performed. We discovered only 354 sex-chromosomal SNPs in 219 transcript sequences (genes). We randomly selected 39 sex-chromosomal genes to examine the reproducibility of the RNA-seq results and observed tight linkage to the male-determining locus in a spinach segregating population (140 individuals). Further analysis using a large-scale population (>1400) and over 100 spinach germplasm accessions and cultivars showed that SNPs in at least 12 genes are fully linked to the male-determining locus, suggesting that the genes reside in the spinach MSY. Synonymous substitution rates of the MSY genes and X homologues predict a recent divergence (0.40 ± 0.08 Mya). Furthermore, synonymous divergence between spinach and its wild relative (S. tetrandra), whose sex chromosomes (XY) originated from a common ancestral chromosome, predicted that the species diverged around 5.7 Mya. Assuming that dioecy in Spinacia evolved before speciation within the genus and has a monophyletic origin, our data suggest that recombination around the spinach sex-determining locus might have stopped significantly later than the evolution of dioecy in Spinacia.

    DOI: 10.1371/journal.pone.0214949

    PubMed

  • Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields

    Akyol Turgut Yigit, Niwa Rieko, Hirakawa Hideki, Maruyama Hayato, Sato Takumi, Suzuki Takae, Fukunaga Ayako, Sato Takashi, Yoshida Shigenobu, Tawaraya Keitaro, Saito Masanori, Ezawa Tatsuhiro, Sato Shusei

    Microbes and Environments   34 ( 1 )   23 - 32   2019   ISSN:13426311 eISSN:13474405

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles  

    <p>Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as an output to investigate the bacterial and fungal communities of roots treated with a commercial AM fungal inoculum in six agricultural fields. AM fungal inoculation significantly influenced the root microbial community structure in all fields. Inoculation changed the abundance of indigenous AM fungi and other fungal members in a field-dependent manner. Inoculation consistently enriched several bacterial OTUs by changing the abundance of indigenous bacteria and introducing new bacteria. Some inoculum-associated bacteria closely interacted with the introduced AM fungi, some of which belonged to the genera <i>Burkholderia</i>, <i>Cellulomonas</i>, <i>Microbacterium</i>, <i>Sphingomonas</i>, and <i>Streptomyces</i> and may be candidate mycorrhizospheric bacteria that contribute to the establishment and/or function of the introduced AM fungi. Inoculated AM fungi also co-occurred with several indigenous bacteria with putative beneficial traits, suggesting that inoculated AM fungi may recruit specific taxa to confer better plant performance. The bacterial families <i>Methylobacteriaceae</i>, <i>Acetobacteraceae</i>, <i>Armatimonadaceae</i>, and <i>Alicyclobacillaceae</i> were consistently reduced by the inoculation, possibly due to changes in the host plant status caused by the inoculum. To the best of our knowledge, this is the first large-scale study to investigate interactions between AM fungal inoculation and indigenous root microbial communities in agricultural fields.</p>

    DOI: 10.1264/jsme2.me18109

    PubMed

    CiNii Research

  • Expression analysis of candidate genes for dioecism and monoecism in spinach

    Sudo Y, Osabe T, Hirakawa H, Suzuki Y, Onodera Y

    Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan   60 ( 0 )   72 - 73   2019   eISSN:24320307

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    Language:Japanese   Publisher:Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  

    DOI: 10.20751/hdanwakai.60.0_72

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  • Killer Applications in Plant GARDEN: Integration of Bioinformatics Tools for Plant Science and Breeding

    GHELFI Andrea, 藤代 継一, 白澤 健太, 原田 大士郎, 小原 光代, 平川 英樹, 田畑 哲之, 磯部 祥子

    トーゴーの日2018   1   2018.10

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    Publisher:バイオサイエンスデータベースセンター  

    DOI: 10.18908/togo2018.p030

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  • 世界における植物ゲノム解析の現状と課題

    原田 大士朗, 市原 寿子, 中谷 明弘, GHELFI Andrea, 藤代 継一, 小原 光代, 平川 英樹, 田畑 哲之, 磯部 祥子

    トーゴーの日2018   1   2018.10

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    DOI: 10.18908/togo2018.p033

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  • 種を超えた植物ゲノム情報統合のためのデータリンク基盤の構築

    市原 寿子, 原田 大士朗, FAWCETT Jeffrey, 白澤 沙知子, 小原 光代, 菊地 正隆, 長谷川 舞衣, 平川 英樹, 磯部 祥子, 田畑 哲之, 中谷 明弘

    1   2018.10

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    DOI: 10.18908/togo2018.p032

    CiNii Research

  • 植物ゲノム情報統合ポータルサイトPlant GARDENの構築

    平川 英樹, 原田 大士朗, GHELFI Andrea, FAWCETT Jeffrey, 白澤 沙知子, 市原 寿子, 中谷 明弘, 磯部 祥子, 田畑 哲之

    1   2018.10

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    DOI: 10.18908/togo2018.p031

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  • Challenge to genomic selection in strawberry at four breeding stations in Japan

    S. Nagano, K. Shirasawa, F. Maeda, M. Watanabe, Y. Noguchi, S. Kataoka, T. Wada, K. Oku, M. Mori, K. Tasaki, K. Iimura, A. Nakaya, T. Yanagi, H. Hirakawa, S. Isobe

    Acta Horticulturae   1203   1 - 8   2018.6   ISSN:0567-7572 eISSN:2406-6168

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    © 2018 International Society for Horticultural Science. All Rights Reserved. There are more than 30 strawberry breeding stations in Japan, which have developed various cultivars with high-quality fruits under heated conditions. Nonetheless, breeders have begun to feel the limitations of conventional breeding methods, and there is a need for more strategic breeding approaches based on genetic information. To address this problem, we developed a next-generation molecular breeding method to improve fruit firmness in strawberries using a combination of genomic selection (GS) and recurrent selection. This approach was developed in conjunction with four breeding stations operated at the National Agriculture and Food Research Organization Institute of Vegetable and Floriculture Science (NARO-IVFS) and Tochigi, Fukuoka and Chiba prefectures. Multiple parental populations were developed at the four breeding stations, and genotyping and phenotyping were performed for GS modelling. Simple sequence repeat (SSR) markers and single nucleotide polymorphisms (SNPs) previously mapped onto linkage maps were used for genotyping. Conventional GS requires genome-wide genotyping for both the training and breeding populations. To decrease the cost and time for genotyping in the breeding population, we used an Ensemble-based genetic and genomic search (EGGS) in order to generate a model with fewer DNA markers. Second-generation populations (G2) exhibiting reduced variation in fruit firmness compared with the original populations have already been developed. The frequencies of targeted genotypes were increased from the initial population (G0) to the second generation (G2). Though many issues remain to be addressed, we expect that our method will open a new avenue for strawberry breeding.

    DOI: 10.17660/ActaHortic.2018.1203.1

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  • Dissection of niche competition between introduced and indigenous arbuscular mycorrhizal fungi with respect to soybean yield responses International journal

    Rieko Niwa, Takuya Koyama, Takumi Sato, Katsuki Adachi, Keitaro Tawaraya, Shusei Sato, Hideki Hirakawa, ShigenobuYoshida, Tatsuhiro Ezawa

    SCIENTIFIC REPORTS   8 ( 1 )   7419 - 7419   2018.5   ISSN:2045-2322

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    Arbuscular mycorrhizal (AM) fungi associate with most land plants and deliver phosphorus to the host. Identification of biotic/abiotic factors that determine crop responses to AM fungal inoculation is an essential step for successful application of the fungi in sustainable agriculture. We conducted three field trials on soybean with a commercial inoculum and developed a new molecular tool to dissect interactions between the inoculum and indigenous fungi on the MiSeq sequencing platform. Regression analysis indicated that sequence read abundance of the inoculum fungus was the most significant factor that determined soybean yield responses to the inoculation, suggesting that dominance of the inoculum fungus is a necessary condition for positive yield responses. Agricultural practices (fallow/cropping in the previous year) greatly affected the colonization levels (i.e. read abundances) of the inoculum fungus via altering the propagule density of indigenous AM fungi. Analysis of niche competition revealed that the inoculum fungus competed mainly with the indigenous fungi that are commonly distributed in the trial sites, probably because their life-history strategy is the same as that of the inoculum fungus. In conclusion, we provide a new framework for evaluating the significance of environmental factors towards successful application of AM fungi in agriculture.

    DOI: 10.1038/s41598-018-25701-4

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    PubMed

  • Genome structure of Rosa multiflora, a wild ancestor of cultivated roses Reviewed International journal

    Noriko Nakamura, Hideki Hirakawa, Shusei Sato, Shungo Otagaki, Shogo Matsumoto, Satoshi Tabata, Yoshikazu Tanaka

    DNA Research   25 ( 2 )   113 - 121   2018.4   ISSN:1756-1663

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press  

    The draft genome sequence of a wild rose (Rosa multiflora Thunb.) was determined using Illumina MiSeq and HiSeq platforms. The total length of the scaffolds was 739,637,845 bp, consisting of 83,189 scaffolds, which was close to the 711 Mbp length estimated by k-mer analysis. N50 length of the scaffolds was 90,830 bp, and extent of the longest was 1,133,259 bp. The average GC content of the scaffolds was 38.9%. After gene prediction, 67,380 candidates exhibiting sequence homology to known genes and domains were extracted, which included complete and partial gene structures. This large number of genes for a diploid plant may reflect heterogeneity of the genome originating from self-incompatibility in R. multiflora. According to CEGMA analysis, 91.9% and 98.0% of the core eukaryotic genes were completely and partially conserved in the scaffolds, respectively. Genes presumably involved in flower color, scent and flowering are assigned. The results of this study will serve as a valuable resource for fundamental and applied research in the rose, including breeding and phylogenetic study of cultivated roses.

    DOI: 10.1093/dnares/dsx042

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  • Molecular insights into the non-recombining nature of the spinach male-determining region. Reviewed International journal

    Tomohiro Kudoh, Mitsuhiko Takahashi, Takayuki Osabe, Atsushi Toyoda, Hideki Hirakawa, Yutaka Suzuki, Nobuko Ohmido, Yasuyuki Onodera

    Molecular genetics and genomics : MGG   293 ( 2 )   557 - 568   2018.4   ISSN:1617-4615

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    Spinach (Spinacia oleracea L.) is a dioecious plant with male heterogametic sex determination and homomorphic sex chromosomes (XY). The dioecism is utilized for producing commercial hybrid seeds, and hence understanding the molecular-genetic basis of the species' sex determining locus is an important issue for spinach breeding. In this study, seven dominant DNA markers were shown to completely co-segregate with the male-determining gene in segregating spinach populations comprising > 1500 plants. In addition, these seven dominant DNA markers were completely associated with the male-determining gene in over 100 spinach germplasm accessions and cultivars. These observations suggest that, in spinach, a Y-chromosomal region around the male-determining locus does not (or almost not) recombine with a counterpart region on the X chromosome. Using five of the seven DNA markers, five bacterial artificial chromosome (BAC) clone contigs with a total length of approximately 690 kbp were constructed. Full sequencing of six representative BAC clones (total insert length 504 kbp) from the five contigs and a transcriptome analysis by RNA-seq revealed that the Y-chromosomal region around the male-determining locus contains large amounts of repetitive elements, suggesting that the region might be poor in gene content. Most of the repeats found in this region are novel Ty1-copia-like and its derivative elements that accumulate predominantly in heterochromatic regions. Our findings may provide valuable insight into spinach genome structure and clues for future research into the evolution of the sex determining locus.

    DOI: 10.1007/s00438-017-1405-2

    PubMed

  • Association studies of seed-yield related traits for Jatropha curcas L. in Mexico Reviewed

    Li Haiyan, Tsuchimoto Suguru, Harada Kyuya, Yamasaki Masanori, Sakai Hiroe, Wada Naoki, Alipour Atefeh, Sasai Tomohiro, Tsunekawa Atsushi, Tsujimoto Hisashi, Ando Takayuki, Tomemori Hisashi, Sato Shusei, Hirakawa Hideki, Pecina-Quintero Victor, Zamarripa Alfredo, Fukui Kiichi

    Tropical Agriculture and Development   62   68 - 77   2018.3

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    DOI: 10.11248/jsta.62.68

  • Mining of the Uncharacterized Cytochrome P450 Genes Involved in Alkaloid Biosynthesis in California Poppy Using a Draft Genome Sequence

    Hori Kentaro, Yamada Yasuyuki, Purwanto Ratmoyo, Minakuchi Yohei, Toyoda Atsushi, Hirakawa Hideki, Sato Fumihiko

    Plant and Cell Physiology   59 ( 2 )   222 - 233   2018.2   ISSN:00320781 eISSN:14719053

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press  

    Land plants produce specialized low molecular weight metabolites to adapt to various environmental stressors, such as UV radiation, pathogen infection, wounding and animal feeding damage. Due to the large variety of stresses, plants produce various chemicals, particularly plant species-specific alkaloids, through specialized biosynthetic pathways. In this study, using a draft genome sequence and querying known biosynthetic cytochrome P450 (P450) enzyme-encoding genes, we characterized the P450 genes involved in benzylisoquinoline alkaloid (BIA) biosynthesis in California poppy (Eschscholzia californica), as P450s are key enzymes involved in the diversification of specialized metabolism. Our in silico studies showed that all identified enzyme-encoding genes involved in BIA biosynthesis were found in the draft genome sequence of approximately 489 Mb, which covered approximately 97% of the whole genome (502 Mb). Further analyses showed that some P450 families involved in BIA biosynthesis, i.e. the CYP80, CYP82 and CYP719 families, were more enriched in the genome of E. californica than in the genome of Arabidopsis thaliana, a plant that does not produce BIAs. CYP82 family genes were highly abundant, so we measured the expression of CYP82 genes with respect to alkaloid accumulation in different plant tissues and two cell lines whose BIA production differs to estimate the functions of the genes. Further characterization revealed two highly homologous P450s (CYP82P2 and CYP82P3) that exhibited 10-hydroxylase activities with different substrate specificities. Here, we discuss the evolution of the P450 genes and the potential for further genome mining of the genes encoding the enzymes involved in BIA biosynthesis.

    DOI: 10.1093/pcp/pcx210

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    CiNii Research

  • Correction: RNA-sequencing-based transcriptome and biochemical analyses of steroidal saponin pathway in a complete set of Allium fistulosum-A. cepa monosomic addition lines. International journal

    Mostafa Abdelrahman, Magdi El-Sayed, Shusei Sato, Hideki Hirakawa, Shin-Ichi Ito, Keisuke Tanaka, Yoko Mine, Nobuo Sugiyama, Yutaka Suzuki, Naoki Yamauchi, Masayoshi Shigyo

    PloS one   13 ( 1 )   e0190813   2018

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    [This corrects the article DOI: 10.1371/journal.pone.0181784.].

    DOI: 10.1371/journal.pone.0190813

    PubMed

  • Inoculum effect of arbuscular mycorrhizal fungi on soybeans grown in long-term bare-fallowed field with low phosphate availability

    Hayashi Masaki, Niwa Rieko, Urashima Yasufumi, Suga Yuko, Sato Shusei, Hirakawa Hideki, Yoshida Shigenobu, Ezawa Tatsuhiro, Karasawa Toshihiko

    Soil Science and Plant Nutrition   64 ( 3 )   306 - 311   2018   ISSN:0038-0768

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    Publisher:Informa UK Limited  

    DOI: 10.1080/00380768.2018.1473007

  • 植物ゲノム統合データベースPGDBjの構築

    平川 英樹, 中谷 明弘, 市原 寿子, 柴谷 多恵子, 浅水 恵理香, 白澤 沙知子, 中村 保一, 磯部 祥子, 田畑 哲之

    トーゴーの日2017   1   2017.10

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    Publisher:バイオサイエンスデータベースセンター  

    DOI: 10.18908/togo2017.p068

    CiNii Research

  • 種を超えたゲノム情報統合のためのデータリンク基盤の構築

    市原 寿子, 菊地 正隆, 長谷川 舞衣, 小原 光代, 平川 英樹, 磯部 祥子, 田畑 哲之, 中谷 明弘

    1   2017.10

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    DOI: 10.18908/togo2017.p069

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  • Development and Characterization of SSR Markers to Study Genetic Diversity and Population Structure of Horsegram Germplasm (Macrotyloma uniflorum)

    R. K. Chahota, Divya Shikha, Maneet Rana, Vikas Sharma, Akshay Nag, T. R. Sharma, J. C. Rana, Hideki Hirakawa, Sachiko Isobe

    PLANT MOLECULAR BIOLOGY REPORTER   35 ( 5 )   550 - 561   2017.10   ISSN:0735-9640 eISSN:1572-9818

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:SPRINGER  

    Development of genomic resources in any crop is the pre-requisite for the construction of linkage map and implementation of molecular breeding strategies to develop superior cultivars. Large number of molecular markers are required to enrich the scanty information available in horsegram (Macrotyloma uniflorum).We employed the next-generation Illumina sequencing platform to develop a large number of microsatellite markers in this species. Of the total 23,305 potential SSRs motifs, 5755 primers were designed. Of these, 1425, 1310, 856, 1276, and 888 were of di-, tri-, tetra-, penta-, and hexa-nucleotide repeats respectively. Thirty polymorphic SSR primers and 24 morphological traits were used in 360 horsegram accessions to detect the genetic diversity and population structure. Thirty primers amplified 170 polymorphic alleles with an average of 5.6 alleles per primer having size 80 to 380 bp. The polymorphism information content (PIC) ranged from 0.15 to 0.76 with an average of 0.50, suggesting that SSR markers used in the study were polymorphic and suitable for characterization of horsegram germplasm. Dendrogram-based on Jaccard's similarity coefficient and neighbor-joining tree grouped the horsegram accessions into two major clusters. Similarly, STRUCTURE analysis assigned genotypes into two gene pools namely Himalayan origin and Southern India. Diversity analysis based on 24 agro-morphological traits also suggested the presence of high level of diversity among the accessions.

    DOI: 10.1007/s11105-017-1045-z

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  • The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding International journal

    Kenta Shirasawa, Kanji Isuzugawa, Mitsunobu Ikenaga, Yutaro Saito, Toshiya Yamamoto, Hideki Hirakawa, Sachiko Isobe

    DNA RESEARCH   24 ( 5 )   499 - 508   2017.10   ISSN:1340-2838 eISSN:1756-1663

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:OXFORD UNIV PRESS  

    We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9Mb sweet cherry genome, as estimated by k-mer analysis, and included>96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A highdensity consensus map with 2,382 loci was constructed using double-digest restriction site-associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map-and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)).

    DOI: 10.1093/dnares/dsx020

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    PubMed

  • Genetic Tracing of Jatropha curcas L. from Its Mesoamerican Origin to the World International journal

    Haiyan Li, Suguru Tsuchimoto, Kyuya Harada, Masanori Yamasaki, Hiroe Sakai, Naoki Wada, Atefeh Alipour, Tomohiro Sasai, Atsushi Tsunekawa, Hisashi Tsujimoto, Takayuki Ando, Hisashi Tomemori, Shusei Sato, Hideki Hirakawa, Victor P. Quintero, Alfredo Zamarripa, Primitivo Santos, Adel Hegazy, Abdalla M. Ali, Kiichi Fukui

    FRONTIERS IN PLANT SCIENCE   8   1539 - 1539   2017.9   ISSN:1664-462X

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:FRONTIERS MEDIA SA  

    Jatropha curcas L. (Jatropha), a shrub species of the family Euphorbiaceae, has been recognized as a promising biofuel plant for reducing greenhouse gas emissions. However, recent attempts at commercial cultivation in Africa and Asia have failed because of low productivity. It is important to elucidate genetic diversity and relationship in worldwide Jatropha genetic resources for breeding of better commercial cultivars. Here, genetic diversity was analyzed by using 246 accessions from Mesoamerica, Africa and Asia, based on 59 simple sequence repeat markers and eight retrotransposon-based insertion polymorphism markers. We found that central Chiapas of Mexico possesses the most diverse genetic resources, and the Chiapas Central Depression could be the center of origin. We identified three genetic groups in Mesoamerica, whose distribution revealed a distinct geographic cline. One of them consists mainly of accessions from central Chiapas. This suggests that it represents the original genetic group. We found two Veracruz accessions in another group, whose ancestors might be shipped from Port of Veracruz to the Old World, to be the source of all African and Asian Jatropha. Our results suggest the human selection that caused low productivity in Africa and Asia, and also breeding strategies to improve African and Asian Jatropha. Cultivars improved in the productivity will contribute to expand mass commercial cultivation of Jatropha in Africa and Asia to increase biofuel production, and finally will support in the battle against the climate change.

    DOI: 10.3389/fpls.2017.01539

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  • Complete Sequence of a Staphylococcus aureus Clonal Complex 81 Strain, the Dominant Lineage in Food Poisoning Outbreaks in Japan. International journal

    Yusuke Sato'o, Junzo Hisatsune, Hideki Hirakawa, Hisaya K Ono, Katsuhiko Omoe, Motoyuki Sugai

    Genome announcements   5 ( 34 )   2017.8   ISSN:2169-8287

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    Staphylococcus aureus No. 10 is an isolate from a staphylococcal food poisoning outbreak in Japan, classified as clonal complex 81 subtype 1. It preferentially produces larger quantities of staphylococcal enterotoxin A (SEA) and staphylococcal enterotoxin H (SEH) in foods and media. Here, we report the complete annotated genome sequence of the chromosome and a plasmid.

    DOI: 10.1128/genomeA.00853-17

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  • Development of genome-wide SSR markers in horsegram and their use for genetic diversity and cross-transferability analysis

    Rahul Kaldate, Maneet Rana, Vikas Sharma, Hideki Hirakawa, Rahul Kumar, Gagandeep Singh, Rakesh Kumar Chahota, Sachiko N. Isobe, Tilak Raj Sharma

    MOLECULAR BREEDING   37 ( 8 )   2017.8   ISSN:1380-3743 eISSN:1572-9788

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    Horsegram [Macrotyloma uniflorum (Lam.) Verdc.] commonly known as kulthi or Madras gram is an important drought tolerant legume crop used as food and fodder in India and across the globe. Horsegram is tolerant to many biotic and abiotic stresses and considered a potential future food legume. Despite being a multiutility crop, insufficient genomic information is available in this species, which is otherwise required for genetic improvement. Hence, in the present work we used next-generation sequencing (NGS) technology for genome-wide development and characterization of novel simple sequence repeat (SSR) markers in horsegram. In all, 2458 SSR primer pairs were designed from NGS data and 117 SSRs were characterized in 48 diverse lines of horsegram. Cross-transferability of these markers was also checked in nine related legume species. The polymorphic SSRs revealed high diversity measures such as mean values of expected heterozygosity (He; 0.54), observed heterozygosity (Ho; 0.64), and polymorphism information content (PIC; 0.46). Analysis of molecular variance (AMOVA) revealed high degree of genetic variance within the populations. Dendrogram based on Jaccard's similarity coefficient and principal component analysis (PCA) revealed two groups in the analyzed accessions. This observation was further confirmed by Bayesian genetic STRUCTURE analysis. The SSR markers developed herein can be used in diverse genetic analysis including association mapping in this crop and also in related legume crops with limited marker resources. Hence, this new SSR dataset can be useful for molecular breeding research in this underutilized pulse crop. In addition, genetic diversity estimates of analyzed germplasm can be important for devising future breeding programmes in horsegram.

    DOI: 10.1007/s11032-017-0701-1

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  • RNA-sequencing-based transcriptome and biochemical analyses of steroidal saponin pathway in a complete set of Allium fistulosum -A. cepa monosomic addition lines Reviewed International journal

    Mostafa Abdelrahman, Magdi El-Sayed, Shusei Sato, Hideki Hirakawa, Shin-ichi Ito, Keisuke Tanaka, Yoko Mine, Nobuo Sugiyama, Minoru Suzuki, Naoki Yamauchi, Masayoshi Shigyo

    PLOS ONE   12 ( 8 )   e0181784   2017.8   ISSN:1932-6203

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    The genus Allium is a rich source of steroidal saponins, and its medicinal properties have been attributed to these bioactive compounds. The saponin compounds with diverse structures play a pivotal role in Allium's defense mechanism. Despite numerous studies on the occurrence and chemical structure of steroidal saponins, their biosynthetic pathway in Allium species is poorly understood. The monosomic addition lines (MALs) of the Japanese bunching onion (A. fistulosum, FF) with an extra chromosome from the shallot (A. cepa Aggregatum group, AA) are powerful genetic resources that enable us to understand many physiological traits of Allium. In the present study, we were able to isolate and identify Alliospiroside A saponin compound in A. fistulosum with extra chromosome 2A from shallot (FF2A) and its role in the defense mechanism against Fusarium pathogens. Furthermore, to gain molecular insight into the Allium saponin biosynthesis pathway, high-throughput RNA-Seq of the root, bulb, and leaf of AA, MALs, and FF was carried out using Illumina's HiSeq 2500 platform. An open access Allium Transcript Database (Allium TDB, http://alliumtdb.kazusa.or.jp) was generated based on RNA-Seq data. The resulting assembled transcripts were functionally annotated, revealing 50 unigenes involved in saponin biosynthesis. Differential gene expression (DGE) analyses of AA and MALs as compared with FF (as a control) revealed a strong up-regulation of the saponin downstream pathway, including cytochrome P450, glycosyltransferase, and beta-glucosidase in chromosome 2A. An understanding of the saponin compounds and biosynthesis-related genes would facilitate the development of plants with unique saponin content and, subsequently, improved disease resistance.

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  • Draft Genome Sequences of the Xylose-Fermenting Yeast Scheffersomyces shehatae NBRC 1983T and a Thermotolerant Isolate of S. shehatae ATY839 (JCM 18690). International journal

    Natsumi Okada, Ayumi Tanimura, Hideki Hirakawa, Masako Takashima, Jun Ogawa, Jun Shima

    Genome announcements   5 ( 20 )   2017.5   ISSN:2169-8287

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    Draft genome sequences of the type strain (NBRC 1983) and a thermotolerant isolate (ATY839) of the xylose-fermenting yeast Scheffersomyces shehatae were determined. The genome sizes and presumed open reading frames were highly similar between strains NBRC 1983T and ATY839.

    DOI: 10.1128/genomeA.00347-17

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  • Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa). International journal

    Soichiro Nagano, Kenta Shirasawa, Hideki Hirakawa, Fumi Maeda, Masami Ishikawa, Sachiko N Isobe

    BMC genomics   18 ( 1 )   374 - 374   2017.5

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    BACKGROUND: The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S1 mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers. RESULTS: The 'Reikou' linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes. CONCLUSIONS: Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

    DOI: 10.1186/s12864-017-3762-y

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  • Complete genome sequencing of newly isolated thermotolerant Corynebacterium glutamicum N24 provides a new insights into its thermotolerant phenotype.

    Matsutani M, Nantapong N, Murata R, Paisrisan P, Hirakawa H, Kataoka N, Yakushi T, Matsushita K

    Journal of biotechnology   247   29 - 33   2017.4   ISSN:0168-1656

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    DOI: 10.1016/j.jbiotec.2017.02.025

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  • Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis Reviewed International journal

    Yuko Makita, Kiaw Kiaw Ng, G. Veera Singham, Mika Kawashima, Hideki Hirakawa, Shusei Sato, Ahmad Sofiman Othman, Minami Matsui

    DNA RESEARCH   24 ( 2 )   159 - 167   2017.4   ISSN:1340-2838 eISSN:1756-1663

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    Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer. With these data, we updated around 5,500 gene structures and newly annotated around 9,500 transcription start sites. Second, to elucidate the rubber biosynthetic pathways and their transcriptional regulation, we carried out tissue- and cultivar-specific RNA-Seq analysis. By using our recently published genome sequence, we confirmed the expression patterns of the rubber biosynthetic genes. Our data suggest that the cytoplasmic mevalonate (MVA) pathway is the main route for isoprenoid biosynthesis in latex production. In addition to the well-studied polymerization factors, we suggest that rubber elongation factor 8 (REF8) is a candidate factor in cis-polyisoprene biosynthesis. We have also identified 39 transcription factors that may be key regulators in latex production. Expression profile analysis using two additional cultivars, RRIM 901 and PB 350, via an RNA-Seq approach revealed possible expression differences between a high latex-yielding cultivar and a disease-resistant cultivar.

    DOI: 10.1093/dnares/dsw056

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  • A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

    Kenta Shirasawa, Masaru Tanaka, Yasuhiro Takahata, Daifu Ma, Qinghe Cao, Qingchang Liu, Hong Zhai, Sang-Soo Kwak, Jae Cheol Jeong, Ung-Han Yoon, Hyeong-Un Lee, Hideki Hirakawa, Sachiko Isobe

    SCIENTIFIC REPORTS   7   44207   2017.3   ISSN:2045-2322

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    Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we used an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.

    DOI: 10.1038/srep44207

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  • A Novel Repressor of the ica Locus Discovered in Clinically Isolated Super-Biofilm-Elaborating Staphylococcus aureus. International journal

    Liansheng Yu, Junzo Hisatsune, Ikue Hayashi, Nobuyuki Tatsukawa, Yusuke Sato'o, Emiri Mizumachi, Fuminori Kato, Hideki Hirakawa, Gerald B Pier, Motoyuki Sugai

    mBio   8 ( 1 )   2017.1   ISSN:2150-7511

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    Staphylococcus aureus TF2758 is a clinical isolate from an atheroma and a super-biofilm-elaborating/polysaccharide intercellular adhesin (PIA)/poly-N-acetylglucosamine (PNAG)-overproducing strain (L. Shrestha et al., Microbiol Immunol 60:148-159, 2016, https://doi.org/10.1111/1348-0421.12359). A microarray analysis and DNA genome sequencing were performed to identify the mechanism underlying biofilm overproduction by TF2758. We found high transcriptional expression levels of a 7-gene cluster (satf2580 to satf2586) and the ica operon in TF2758. Within the 7-gene cluster, a putative transcriptional regulator gene designated rob had a nonsense mutation that caused the truncation of the protein. The complementation of TF2758 with rob from FK300, an rsbU-repaired derivative of S. aureus strain NCTC8325-4, significantly decreased biofilm elaboration, suggesting a role for rob in this process. The deletion of rob in non-biofilm-producing FK300 significantly increased biofilm elaboration and PIA/PNAG production. In the search for a gene(s) in the 7-gene cluster for biofilm elaboration controlled by rob, we identified open reading frame (ORF) SAOUHSC_2898 (satf2584). Our results suggest that ORF SAOUHSC_2898 (satf2584) and icaADBC are required for enhanced biofilm elaboration and PIA/PNAG production in the rob deletion mutant. Rob bound to a palindromic sequence within its own promoter region. Furthermore, Rob recognized the TATTT motif within the icaR-icaA intergenic region and bound to a 25-bp DNA stretch containing this motif, which is a critically important short sequence regulating biofilm elaboration in S. aureus Our results strongly suggest that Rob is a long-sought repressor that recognizes and binds to the TATTT motif and is an important regulator of biofilm elaboration through its control of SAOUHSC_2898 (SATF2584) and Ica protein expression in S. aureus IMPORTANCE: During the search for molecular mechanisms underlying biofilm overproduction of Staphylococcus aureus TF2758, we found a putative transcriptional regulator gene designated rob within a 7-gene cluster showing a high transcriptional expression level by microarray analysis. The deletion of rob in non-biofilm-producing FK300, an rsbU-repaired derivative of NCTC8325-4, significantly increased biofilm elaboration and PIA/PNAG production. The search for a gene(s) in the 7-gene cluster for biofilm elaboration controlled by rob identified ORF SAOUHSC_2898. Besides binding to its own promoter region to control ORF SAOUHSC_2898 expression, Rob recognized the TATTT motif within the icaR-icaA intergenic region and bound to a 25-bp DNA stretch containing this motif, which is a critically important short sequence regulating biofilm elaboration in S. aureus Our results strongly suggest that Rob is a long-sought repressor that recognizes and binds to the TATTT motif and is a new important regulator of biofilm elaboration through its control of SAOUHSC_2898 and Ica protein expression in S. aureus.

    DOI: 10.1128/mBio.02282-16

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  • Challenges to genome sequence dissection in sweetpotato.

    Isobe S, Shirasawa K, Hirakawa H

    Breeding science   67 ( 1 )   35 - 40   2017.1   ISSN:1344-7610

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    DOI: 10.1270/jsbbs.16186

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  • Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation. International journal

    Parwinder Kaur, Rudi Appels, Philipp E Bayer, Gabriel Keeble-Gagnere, Jiankang Wang, Hideki Hirakawa, Kenta Shirasawa, Philip Vercoe, Katia Stefanova, Zoey Durmic, Phillip Nichols, Clinton Revell, Sachiko N Isobe, David Edwards, William Erskine

    Frontiers in plant science   8   1463 - 1463   2017

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    Mitigating methane production by ruminants is a significant challenge to global livestock production. This research offers a new paradigm to reduce methane emissions from ruminants by breeding climate-clever clovers. We demonstrate wide genetic diversity for the trait methanogenic potential in Australia's key pasture legume, subterranean clover (Trifolium subterraneum L.). In a bi-parental population the broadsense heritability in methanogenic potential was moderate (H2 = 0.4) and allelic variation in a region of Chr 8 accounted for 7.8% of phenotypic variation. In a genome-wide association study we identified four loci controlling methanogenic potential assessed by an in vitro fermentation system. Significantly, the discovery of a single nucleotide polymorphism (SNP) on Chr 5 in a defined haplotype block with an upstream putative candidate gene from a plant peroxidase-like superfamily (TSub_g18548) and a downstream lectin receptor protein kinase (TSub_g18549) provides valuable candidates for an assay for this complex trait. In this way haplotype variation can be tracked to breed pastures with reduced methanogenic potential. Of the quantitative trait loci candidates, the DNA-damage-repair/toleration DRT100-like protein (TSub_g26967), linked to avoid the severity of DNA damage induced by secondary metabolites, is considered central to enteric methane production, as are disease resistance (TSub_g26971, TSub_g26972, and TSub_g18549) and ribonuclease proteins (TSub_g26974, TSub_g26975). These proteins are good pointers to elucidate the genetic basis of in vitro microbial fermentability and enteric methanogenic potential in subterranean clover. The genes identified allow the design of a suite of markers for marker-assisted selection to reduce rumen methane emission in selected pasture legumes. We demonstrate the feasibility of a plant breeding approach without compromising animal productivity to mitigate enteric methane emissions, which is one of the most significant challenges to global livestock production.

    DOI: 10.3389/fpls.2017.01463

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  • Establishment of a genome-wide and quantitative protocol for assessment of transcriptional activity at human retrotransposon L1 antisense promoters

    Ishiguro Koichi, Higashino Saneyuki, Hirakawa Hideki, Sato Shusei, Aizawa Yasunori

    Genes & Genetic Systems   92 ( 5 )   243 - 249   2017   ISSN:13417568 eISSN:18805779

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    <p>Long interspersed element 1 (L1) retrotransposon sequences are widespread in the human genome, occupying ~500,000 locations. The majority of L1s have lost their retrotransposition capability, although a significant population of human L1s maintains bidirectional transcriptional activity from the internal promoter. While the sense promoter drives transcription of the entire L1 mRNA and leads to L1 retrotransposition, the antisense promoter (ASP) transcribes L1-gene chimeric RNAs that include neighboring exon sequences. Activation mechanisms and functional impacts of L1ASP transcription are thought to vary at every L1ASP location. To explore the locus-specific regulation and function of L1ASP transcription, quantitative methodology is necessary for identifying the genomic positions of highly active L1ASPs on a genome-wide scale. Here, we employed deep-sequencing techniques and built a 3’ RACE-based experimental and bioinformatics protocol, named the L1 antisense transcriptome protocol (LATRAP). In LATRAP, the PCR primer and the read mapping scheme were designed to reduce false positives and negatives, which may have been included as hits in previous cloning studies. LATRAP was here applied to the A549 human lung cancer cell line, and 313 L1ASP loci were detected to have transcriptional activity but differed in the number of mapped reads by four orders of magnitude. This indicates that transcriptional activities of the individual L1ASPs can vary greatly and that only a small population of L1ASP loci is active within individual nuclei. LATRAP is the first experimental method for ranking L1ASPs according to their transcriptional activity and will thus open a new avenue to unveiling the locus-specific biology of L1ASPs.</p>

    DOI: 10.1266/ggs.16-00053

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  • Complete genome sequence of super biofilm-elaborating Staphylococcus aureus isolated in Japan Reviewed International journal

    Liansheng Yu, Junzo Hisatsune, Hideki Hirakawa, Emiri Mizumachi, Atsushi Toyoda, Koji Yahara, Motoyuki Sugai

    Genome Announcements   5 ( 41 )   2017   ISSN:2169-8287

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    Staphylococcus aureus JP080, previously named TF2758, is a clinical isolate from an atheroma and a super biofilm-elaborating strain whose biofilm elaboration is dependent solely on polysaccharide poly-N-acetylglucosamine/polysaccharide intercellular adhesin (PNAG/PIA). Here, we report the complete genome sequence of strain JP080, which consists of one chromosome and one circular plasmid.

    DOI: 10.1128/genomeA.01043-17

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  • Plant Genome DataBase Japan (PGDBj).

    Nakaya A, Ichihara H, Asamizu E, Shirasawa S, Nakamura Y, Tabata S, Hirakawa H

    Methods in molecular biology (Clifton, N.J.)   1533   45 - 77   2017   ISSN:1064-3745

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    DOI: 10.1007/978-1-4939-6658-5_3

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  • Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties Reviewed

    Yasuo Yasui, Hideki Hirakawa, Tetsuo Oikawa, Masami Toyoshima, Chiaki Matsuzaki, Mariko Ueno, Nobuyuki Mizuno, Yukari Nagatoshi, Tomohiro Imamura, Manami Miyago, Kojiro Tanaka, Kazuyuki Mise, Tsutomu Tanaka, Hiroharu Mizukoshi, Masashi Mori, Yasunari Fujita

    DNA RESEARCH   23 ( 6 )   535 - 546   2016.12   ISSN:1340-2838 eISSN:1756-1663

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    Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution.

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  • Target amplicon sequencing for genotyping genome-wide single nucleotide polymorphisms identified by whole-genome resequencing in peanut

    Kenta Shirasawa, Chikara Kuwata, Manabu Watanabe, Masanobu Fukami, Hideki Hirakawa, Sachiko Isobe

    Plant Genome   9 ( 3 )   2016.11   ISSN:1940-3372 eISSN:1940-3372

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    © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA. Genome-wide genotyping data regarding breeding materials are essential resources for improving breeding efficiency, especially in plants with complex genomes with a high degree of polyploidy. Several current breeding efforts in cultivated peanut (Arachis hypogaea L.), which has a tetraploid genome, are devoted to developing high oleic acid cultivars. Genetic maps for such breeding programs have been developed using simple-sequence repeat (SSR) markers, the use of which requires time-consuming electrophoretic analyses. Next-generation sequencing (NGS) technology can overcome this technical hurdle. Initially, we attempted double-digest restriction siteassociated DNA sequencing on peanut breeding materials used to develop high oleic acid cultivars. However, this method was not effective because few single nucleotide polymorphism (SNPs) were available because of low genetic diversity of the lines. The genome sequences of the probable diploid ancestors of cultivated peanut, A. duranensis Krapov. & W. C. Greg. and A. ipaënsis Krapov. & W. C. Greg., are available. Therefore, we next employed whole-genome resequencing analysis to obtain genome-wide SNP data. In this analysis, we observed large biases in the numbers and genomic positions of interspecific and intraspecific SNPs. For genome-wide genotyping, we selected a subset of SNPs covering the peanut genome as the targets of amplicon sequencing analysis. Using this technique, genomewide genotypes of the breeding materials were easily and rapidly determined. The SNP information and analytic methods developed in this study should accelerate genetics, genomics, and breeding in peanut.

    DOI: 10.3835/plantgenome2016.06.0052

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  • 植物ゲノム情報活用のための統合研究基盤の構築

    柴谷 多恵子, 市原 寿子, 白澤 沙知子, 中村 保一, 中谷 明弘, 浅水 恵理香, 平川 英樹, 田畑 哲之

    1   2016.10

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    DOI: 10.18908/togo2016.p020

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  • Blue Light Perception by Both Roots and Rhizobia Inhibits Nodule Formation in Lotus japonicus Reviewed

    Aya Shimomura, Ayumi Naka, Nobuyuki Miyazaki, Sayaka Moriuchi, Susumu Arima, Shusei Sato, Hideki Hirakawa, Makoto Hayashi, Maskit Maymon, Ann M. Hirsch, Akihiro Suzukit

    MOLECULAR PLANT-MICROBE INTERACTIONS   29 ( 10 )   786 - 796   2016.10   ISSN:0894-0282 eISSN:1943-7706

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    In many legumes, roots that are exposed to light do not form nodules. Here, we report that blue light inhibits nodulation in Lotus japonicus roots inoculated with Mesorhizobium loti. Using RNA interference, we suppressed the expression of the phototropin and cryptochrome genes in L. japonicus hairy roots. Under blue light, plants transformed with an empty vector did not develop nodules, whereas plants exhibiting suppressed expression of cry1 and cry2 genes formed nodules. We also measured rhizobial growth to investigate whether the inhibition of nodulation could be caused by a reduced population of rhizobia in response to light. Although red light had no effect on rhizobial growth, blue light had a strong inhibitory effect. Rhizobial growth under blue light was partially restored in signature-tagged mutagenesis (STM) strains in which LOY-HK/PAS- and photolyase-related genes were disrupted. Moreover, when Ljcry1A and Ljcry2B-silenced plants were inoculated with the STM strains, nodulation was additively increased. Our data show that blue light receptors in both the host plant and the symbiont have a profound effect on nodule development. The exact mechanism by which these photomorphogenetic responses function in the symbiosis needs further study, but they are clearly involved in optimizing legume nodulation.

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  • High-resolution genetic maps of Lotus japonicus and L-burttii based on re-sequencing of recombinant inbred lines Reviewed

    Niraj Shah, Hideki Hirakawa, Shohei Kusakabe, Niels Sandal, Jens Stougaard, Mikkel Heide Schierup, Shusei Sato, Stig Uggerhoj Andersen

    DNA RESEARCH   23 ( 5 )   487 - 494   2016.10   ISSN:1340-2838 eISSN:1756-1663

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    Recombinant inbred lines (RILs) derived from bi-parental populations are stable genetic resources, which are widely used for constructing genetic linkage maps. These genetic maps are essential for QTL mapping and can aid contig and scaffold anchoring in the final stages of genome assembly. In this study, two Lotus sp. RIL populations, Lotus japonicus MG-20 x Gifu and Gifu x L. burttii, were characterized by Illumina re-sequencing. Genotyping of 187 MG-20 x Gifu RILs at 87,140 marker positions and 96 Gifu x L. burttii RILs at 357,973 marker positions allowed us to accurately identify 1,929 recombination breakpoints in the MG-20 x Gifu RILs and 1,044 breakpoints in the Gifu x L. burttii population. The resulting high-density genetic maps now facilitate high-accuracy QTL mapping, identification of reference genome mis-assemblies, and characterization of structural variants.

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  • The LORE1 insertion mutant resource Reviewed

    Anna Malolepszy, Terry Mun, Niels Sandal, Vikas Gupta, Manu Dubin, Dorian Urbanski, Niraj Shah, Asger Bachmann, Eigo Fukai, Hideki Hirakawa, Satoshi Tabata, Marcin Nadzieja, Katharina Markmann, Junyi Su, Yosuke Umehara, Takashi Soyano, Akira Miyahara, Shusei Sato, Makoto Hayashi, Jens Stougaard, Stig U. Andersen

    PLANT JOURNAL   88 ( 2 )   306 - 317   2016.10   ISSN:0960-7412 eISSN:1365-313X

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    Long terminal repeat (LTR) retrotransposons are closely related to retroviruses, and their activities shape eukaryotic genomes. Here, we present a complete Lotus japonicus insertion mutant collection generated by identification of 640 653 new insertion events following de novo activation of the LTR element Lotus retrotransposon 1 (LORE1) (http://lotus.au.dk). Insertion preferences are critical for effective gene targeting, and we exploit our large dataset to analyse LTR element characteristics in this context. We infer the mechanism that generates the consensus palindromes typical of retroviral and LTR retrotransposon insertion sites, identify a short relaxed insertion site motif, and demonstrate selective integration into CHG-hypomethylated genes. These characteristics result in a steep increase in deleterious mutation rate following activation, and allow LORE1 active gene targeting to approach saturation within a population of 134 682 L. japonicus lines. We suggest that saturation mutagenesis using endogenous LTR retrotransposons with germinal activity can be used as a general and cost-efficient strategy for generation of non-transgenic mutant collections for unrestricted use in plant research.

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  • Whole-Genome Sequence of the Nitrogen-Fixing Symbiotic Rhizobium Mesorhizobium loti Strain TONO

    Yoshikazu Shimoda, Hideki Hirakawa, Shusei Sato, Kazuhiko Saeki, Makoto Hayashi

    Genome Announcements   4 ( 5 )   2016.9   ISSN:2169-8287 eISSN:2169-8287

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    <italic>Mesorhizobium loti</italic>
    is the nitrogen-fixing microsymbiont for legumes of the genus
    <italic>Lotus</italic>
    . Here, we report the whole-genome sequence of a
    <italic>Mesorhizobium loti</italic>
    strain, TONO, which is used as a symbiont for the model legume
    <italic>Lotus japonicus</italic>
    . The whole-genome sequence of the strain TONO will be a solid platform for comparative genomics analyses and for the identification of genes responsible for the symbiotic properties of
    <italic>Mesorhizobium</italic>
    species.

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  • Draft genome sequence of subterranean clover, a reference for genus Trifolium. International journal

    Hideki Hirakawa, Parwinder Kaur, Kenta Shirasawa, Phillip Nichols, Soichiro Nagano, Rudi Appels, William Erskine, Sachiko N Isobe

    Scientific reports   6   30358 - 30358   2016.8   ISSN:2045-2322

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    Clovers (genus Trifolium) are widely cultivated across the world as forage legumes and make a large contribution to livestock feed production and soil improvement. Subterranean clover (T. subterraneum L.) is well suited for genomic and genetic studies as a reference species in the Trifolium genus, because it is an annual with a simple genome structure (autogamous and diploid), unlike the other economically important perennial forage clovers, red clover (T. pratense) and white clover (T. repens). This report represents the first draft genome sequence of subterranean clover. The 471.8 Mb assembled sequence covers 85.4% of the subterranean clover genome and contains 42,706 genes. Eight pseudomolecules of 401.1 Mb in length were constructed, based on a linkage map consisting of 35,341 SNPs. The comparative genomic analysis revealed that different clover chromosomes showed different degrees of conservation with other Papilionoideae species. These results provide a reference for genetic and genomic analyses in the genus Trifolium and new insights into evolutionary divergence in Papilionoideae species.

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  • Complete Genome Sequence of Moraxella osloensis Strain KMC41, a Producer of 4-Methyl-3-Hexenoic Acid, a Major Malodor Compound in Laundry. International journal

    Takatsugu Goto, Hideki Hirakawa, Yuji Morita, Junko Tomida, Jun Sato, Yuta Matsumura, Asako Mitani, Yu Niwano, Kohei Takeuchi, Hiromi Kubota, Yoshiaki Kawamura

    Genome announcements   4 ( 4 )   2016.7   ISSN:2169-8287 eISSN:2169-8287

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    We report the complete genome sequence of Moraxella osloensis strain KMC41, isolated from laundry with malodor. The KMC41 genome comprises a 2,445,556-bp chromosome and three plasmids. A fatty acid desaturase and at least four β-oxidation-related genes putatively associated with 4-methyl-3-hexenoic acid generation were detected in the KMC41 chromosome.

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  • Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes. International journal

    Yasuo Yasui, Hideki Hirakawa, Mariko Ueno, Katsuhiro Matsui, Tomoyuki Katsube-Tanaka, Soo Jung Yang, Jotaro Aii, Shingo Sato, Masashi Mori

    DNA research : an international journal for rapid publication of reports on genes and genomes   23 ( 3 )   215 - 224   2016.6   ISSN:1340-2838 eISSN:1756-1663

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    Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits.

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  • The Complete Chloroplast Genome Sequence of Zoysia matrella (L.) Merr. Reviewed

    Hidenori Tanaka, Hideki Hirakawa, Melody Muguerza, Masatsugu Hashiguchi, Satoshi Tabata, Ryo Akashi, Shusei Sato

    CROP SCIENCE   56 ( 3 )   1206 - 1212   2016.5   ISSN:0011-183X eISSN:1435-0653

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    Zoysia Willd. include one of the best-known turf-grasses worldwide owing to its adaptability in a wide range of environments and its tolerance to abiotic stresses including soil salinity, soil acidity, cold, drought, and heat. Here, we report the complete chloroplast genome sequence of Zoysia matrella (L.) Merr. obtained by a combination of 454 pyrosequencing and Sanger sequencing platforms. The entire chloroplast genome of Zoysia maps as a circular molecule of 135,810 bp built with a quadripartite organization: two inverted repeats (IRs) of 20,960 bp separated by a large single copy (LSC) sequence of 81,306 bp and a small single copy (SSC) sequence of 12,584 bp. The genome contains 131 unique genes, of which 20 are duplicated in the IRs. We identified a total of 42 simple sequence repeat (SSR) markers with 3 10 repeated nucleotides. Phylogenetic analysis revealed a close relationship between Zoysia and Neyraudia. This study identified genes, insertion-deletion (InDel), and SSR markers that may be useful in inferring evolutionary relationships at both the intra-and interspecific levels. Moreover, the Zoysia chloroplast genome sequence will be helpful in understanding phylogenetic and evolutionary relationships with other species in the Poaceae family and the Chloridoideae subfamily and will be valuable for biogenetic engineering, plant breeding, and ecological conservation.

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  • Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato

    Kenta Shirasawa, Hideki Hirakawa, Sachiko Isobe

    DNA RESEARCH   23 ( 2 )   145 - 153   2016.4   ISSN:1340-2838 eISSN:1756-1663

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    Double-digest restriction site-associated DNA sequencing (ddRAD-Seq) enables high-throughput genome-wide genotyping with next-generation sequencing technology. Consequently, this method has become popular in plant genetics and breeding. Although computational in silico prediction of restriction sites from the genome sequence is recognized as an effective approach for choosing the restriction enzymes to be used, few reports have evaluated the in silico predictions in actual experimental data. In this study, we designed and demonstrated a workflow for in silico and empirical ddRAD-Seq analysis in tomato, as follows: (i) in silico prediction of optimum restriction enzymes from the reference genome, (ii) verification of the prediction by actual ddRAD-Seq data of four restriction enzyme combinations, (iii) establishment of a computational data processing pipeline for high-confidence single nucleotide polymorphism (SNP) calling, and (iv) validation of SNP accuracy by construction of genetic linkage maps. The quality of SNPs based on de novo assembly reference of the ddRAD-Seq reads was comparable with that of SNPs obtained using the published reference genome of tomato. Comparisons of SNP calls in diverse tomato lines revealed that SNP density in the genome influenced the detectability of SNPs by ddRAD-Seq. In silico prediction prior to actual analysis contributed to optimization of the experimental conditions for ddRAD-Seq, e.g. choices of enzymes and plant materials. Following optimization, this ddRAD-Seq pipeline could help accelerate genetics, genomics, and molecular breeding in both model and non-model plants, including crops.

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  • Sequencing and comparative analyses of the genomes of zoysiagrasses Reviewed

    Hidenori Tanaka, Hideki Hirakawa, Shunichi Kosugi, Shinobu Nakayama, Akiko Ono, Akiko Watanabe, Masatsugu Hashiguchi, Takahiro Gondo, Genki Ishigaki, Melody Muguerza, Katsuya Shimizu, Noriko Sawamura, Takayasu Inoue, Yuichi Shigeki, Naoki Ohno, Satoshi Tabata, Ryo Akashi, Shusei Sato

    DNA RESEARCH   23 ( 2 )   171 - 180   2016.4   ISSN:1340-2838 eISSN:1756-1663

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    Zoysia is a warm-season turfgrass, which comprises 11 allotetraploid species (2n = 4x = 40), each possessing different morphological and physiological traits. To characterize the genetic systems of Zoysia plants and to analyse their structural and functional differences in individual species and accessions, we sequenced the genomes of Zoysia species using HiSeq and MiSeq platforms. As a reference sequence of Zoysia species, we generated a high-quality draft sequence of the genome of Z. japonica accession 'Nagirizaki' (334 Mb) in which 59,271 protein-coding genes were predicted. In parallel, draft genome sequences of Z. matrella 'Wakaba' and Z. pacifica 'Zanpa' were also generated for comparative analyses. To investigate the genetic diversity among the Zoysia species, genome sequence reads of three additional accessions, Z. japonica 'Kyoto', Z. japonica 'Miyagi' and Z. matrella 'Chiba Fair Green', were accumulated, and aligned against the reference genome of 'Nagirizaki' along with those from 'Wakaba' and 'Zanpa'. As a result, we detected 7,424,163 single-nucleotide polymorphisms and 852,488 short indels among these species. The information obtained in this study will be valuable for basic studies on zoysiagrass evolution and genetics as well as for the breeding of zoysiagrasses, and is made available in the 'Zoysia Genome Database' at .

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  • A simulation-based breeding design that uses whole-genome prediction in tomato Reviewed International journal

    Eiji Yamamoto, Hiroshi Matsunaga, Akio Onogi, Hiromi Kajiya-Kanegae, Mai Minamikawa, Akinori Suzuki, Kenta Shirasawa, Hideki Hirakawa, Tsukasa Nunome, Hirotaka Yamaguchi, Koji Miyatake, Akio Ohyama, Hiroyoshi Iwata, Hiroyuki Fukuoka

    SCIENTIFIC REPORTS   6   19454 - 19454   2016.1   ISSN:2045-2322

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    Efficient plant breeding methods must be developed in order to increase yields and feed a growing world population, as well as to meet the demands of consumers with diverse preferences who require high-quality foods. We propose a strategy that integrates breeding simulations and phenotype prediction models using genomic information. The validity of this strategy was evaluated by the simultaneous genetic improvement of the yield and flavour of the tomato (Solanum lycopersicum), as an example. Reliable phenotype prediction models for the simulation were constructed from actual genotype and phenotype data. Our simulation predicted that selection for both yield and flavour would eventually result in morphological changes that would increase the total plant biomass and decrease the light extinction coefficient, an essential requirement for these improvements. This simulation-based genome-assisted approach to breeding will help to optimise plant breeding, not only in the tomato but also in other important agricultural crops.

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  • Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato International journal

    Kenta Shirasawa, Hideki Hirakawa, Tsukasa Nunome, Satoshi Tabata, Sachiko Isobe

    PLANT BIOTECHNOLOGY JOURNAL   14 ( 1 )   51 - 60   2016.1   ISSN:1467-7644 eISSN:1467-7652

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    Genome-wide mutations induced by ethyl methanesulfonate (EMS) and gamma irradiation in the tomato Micro-Tom genome were identified by a whole-genome shotgun sequencing analysis to estimate the spectrum and distribution of whole-genome DNA mutations and the frequency of deleterious mutations. A total of similar to 370 Gb of paired-end reads for four EMS-induced mutants and three gamma-ray-irradiated lines as well as a wild-type line were obtained by next-generation sequencing technology. Using bioinformatics analyses, we identified 5920 induced single nucleotide variations and insertion/deletion (indel) mutations. The predominant mutations in the EMS mutants were C/G to T/A transitions, while in the gamma-ray mutants, C/G to T/A transitions, A/T to T/A transversions, A/T to G/C transitions and deletion mutations were equally common. Biases in the base composition flanking mutations differed between the mutagenesis types. Regarding the effects of the mutations on gene function, >90% of the mutations were located in intergenic regions, and only 0.2% were deleterious. In addition, we detected 1 140 687 spontaneous single nucleotide polymorphisms and indel polymorphisms in wild-type Micro-Tom lines. We also found copy number variation, deletions and insertions of chromosomal segments in both the mutant and wild-type lines. The results provide helpful information not only for mutation research, but also for mutant screening methodology with reverse-genetic approaches.

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  • Comparison of Spinach Sex Chromosomes with Sugar Beet Autosomes Reveals Extensive Synteny and Low Recombination at the Male-Determining Locus

    Satoshi Takahata, Takumi Yago, Keisuke Iwabuchi, Hideki Hirakawa, Yutaka Suzuki, Yasuyuki Onodera

    Journal of Heredity   107 ( 7 )   679 - 685   2016   ISSN:0022-1503 eISSN:1465-7333

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    DOI: 10.1093/jhered/esw055

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  • Complete Genome Sequencing and Comparative Genomic Analysis of the Thermotolerant Acetic Acid Bacterium, <i>Acetobacter pasteurianus</i> SKU1108, Provide a New Insight into Thermotolerance

    Matsutani Minenosuke, Hirakawa Hideki, Hiraoka Eri, Theeragool Gunjana, Yakushi Toshiharu, Matsushita Kazunobu

    Microbes and Environments   31 ( 4 )   395 - 400   2016   ISSN:13426311 eISSN:13474405

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    <p><i>Acetobacter pasteurianus</i> SKU1108 is a typical thermotolerant acetic acid bacterium. In this study, the complete genome sequence of the SKU1108 strain was elucidated, and information on genomic modifications due to the thermal adaptation of SKU1108 was updated. In order to obtain a clearer understanding of the genetic background responsible for thermotolerance, the SKU1108 genome was compared with those of two closely related complete genome strains, thermotolerant <i>A. pasteurianus</i> 386B and mesophilic <i>A. pasteurianus</i> NBRC 3283. All 24 “thermotolerant genes” required for growth at higher temperatures in the thermotolerant <i>Acetobacter tropicalis</i> SKU1100 strain were conserved in all three strains. However, these thermotolerant genes accumulated amino acid mutations. Some biased mutations, particularly those that occurred in xanthine dehydrogenase XdhA, may be related to thermotolerance. By aligning whole genome sequences, we identified ten SKU1108 strain-specific regions, three of which were conserved in the genomes of the two thermotolerant <i>A. pasteurianus</i> strains. One of the regions contained a unique paralog of the thermotolerant gene <i>xdhA</i>, which may also be responsible for conferring thermotolerance. Thus, comparative genomics of complete genome sequences may provide novel insights into the phenotypes of these thermotolerant strains.</p>

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  • GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments. International journal

    Shunichi Kosugi, Hideki Hirakawa, Satoshi Tabata

    Bioinformatics (Oxford, England)   31 ( 23 )   3733 - 3741   2015.12   ISSN:1367-4803 eISSN:1460-2059

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    MOTIVATION: Genome assemblies generated with next-generation sequencing (NGS) reads usually contain a number of gaps. Several tools have recently been developed to close the gaps in these assemblies with NGS reads. Although these gap-closing tools efficiently close the gaps, they entail a high rate of misassembly at gap-closing sites. RESULTS: We have found that the assembly error rates caused by these tools are 20-500-fold higher than the rate of errors introduced into contigs by de novo assemblers. We here describe GMcloser, a tool that accurately closes these gaps with a preassembled contig set or a long read set (i.e., error-corrected PacBio reads). GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap closure. We demonstrate with sequencing data from various organisms that the gap-closing accuracy of GMcloser is 3-100-fold higher than those of other available tools, with similar efficiency. AVAILABILITY AND IMPLEMENTATION: GMcloser and an accompanying tool (GMvalue) for evaluating the assembly and correcting misassemblies except SNPs and short indels in the assembly are available at https://sourceforge.net/projects/gmcloser/. CONTACT: shunichi.kosugi@riken.jp. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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  • Functional and expression analyses of transcripts based on full-length cDNAs of Sorghum bicolor Reviewed

    Setsuko Shimada, Yuko Makita, Tomoko Kuriyama-Kondou, Mika Kawashima, Yoshiki Mochizuki, Hideki Hirakawa, Shusei Sato, Tetsuro Toyoda, Minami Matsui

    DNA RESEARCH   22 ( 6 )   485 - 493   2015.12   ISSN:1340-2838 eISSN:1756-1663

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    Sorghum bicolor is one of the most important crops for food and bioethanol production. Its small diploid genome and resistance to environmental stress make sorghum an attractive model for studying the functional genomics of the Saccharinae and other C-4 grasses. We analyzed the domain-based functional annotation of the cDNAs using the gene ontology (GO) categories for molecular function to characterize all the genes cloned in the full-length cDNA library of sorghum. The sorghum cDNA library successfully captured a wide range of cDNA-encoded proteins with various functions. To characterize the protein function of newly identified cDNAs, a search of their deduced domains and comparative analyses in the Oryza sativa and Zea mays genomes were carried out. Furthermore, genes on the sense strand corresponding to antisense transcripts were classified based on the GO of molecular function. To add more information about these genes, we have analyzed the expression profiles using RNA-Seq of three tissues (spikelet, seed and stem) during the starch-filling phase. We performed functional analysis of tissue-specific genes and expression analysis of genes of starch biosynthesis enzymes. This functional analysis of sorghum full-length cDNAs and the transcriptome information will facilitate further analysis of the Saccharinae and grass families.

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  • Draft Genome Sequence of Porphyromonas gingivalis Strain Ando Expressing a 53-Kilodalton-Type Fimbrilin Variant of Mfa1 Fimbriae. International journal

    Takatsugu Goto, Keiji Nagano, Hideki Hirakawa, Kaori Tanaka, Fuminobu Yoshimura

    Genome announcements   3 ( 6 )   2015.11   ISSN:2169-8287 eISSN:2169-8287

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    Periodontopathic Porphyromonas gingivalis strain Ando abundantly expresses a 53-kDa-type Mfa1 fimbria. Here, we report the draft genome sequence of Ando, with a size of 2,229,994 bp, average G+C content of 48.4%, and 1,755 predicted protein-coding sequences.

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  • Complete genome and gene expression analyses of Asaia bogorensis reveal unique responses to culture with mammalian cells as a potential opportunistic human pathogen Reviewed International journal

    Mikihiko Kawai, Norie Higashiura, Kimie Hayasaki, Naruhei Okamoto, Akiko Takami, Hideki Hirakawa, Kazunobu Matsushita, Yoshinao Azuma

    DNA RESEARCH   22 ( 5 )   357 - 366   2015.10   ISSN:1340-2838 eISSN:1756-1663

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    Asaia bogorensis, a member of acetic acid bacteria (AAB), is an aerobic bacterium isolated from flowers and fruits, as well as an opportunistic pathogen that causes human peritonitis and bacteraemia. Here, we determined the complete genomic sequence of the As. bogorensis type strain NBRC 16594, and conducted comparative analyses of gene expression under different conditions of co-culture with mammalian cells and standard AAB culture. The genome of As. bogorensis contained 2,758 protein-coding genes within a circular chromosome of 3,198,265 bp. There were two complete operons encoding cytochrome bo(3)-type ubiquinol terminal oxidases: cyoABCD-1 and cyoABCD-2. The cyoABCD-1 operon was phylogenetically common to AAB genomes, whereas the cyoABCD-2 operon belonged to a lineage distinctive from the cyoABCD-1 operon. Interestingly, cyoABCD-1 was less expressed under co-culture conditions than under the AAB culture conditions, whereas the converse was true for cyoABCD-2. Asaia bogorensis shared pathogenesis-related genes with another pathogenic AAB, Granulibacter bethesdensis, including a gene coding pathogen-specific large bacterial adhesin and additional genes for the inhibition of oxidation and antibiotic resistance. Expression alteration of the respiratory chain and unique hypothetical genes may be key traits that enable the bacterium to survive under the co-culture conditions.

    DOI: 10.1093/dnares/dsv018

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  • Integrating transcriptome and target metabolome variability in doubled haploids of Allium cepa for abiotic stress protection

    Abdelrahman Mostafa, Sawada Yuji, Nakabayashi Ryo, Sato Shusei, Hirakawa Hideki, El-Sayed Magdi, Yokota Hirai Masami, Saito Kazuki, Yamauchi Naoki, Shigyo Masayoshi

    Molecular Breeding   35 ( 10 )   195 - 195   2015.10   ISSN:1380-3743 eISSN:1572-9788

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  • Gene Expression Profiles in Jatropha Under Drought Stress and During Recovery

    Joyce A. Cartagena, Motoaki Seki, Maho Tanaka, Takaki Yamauchi, Shusei Sato, Hideki Hirakawa, Takashi Tsuge

    PLANT MOLECULAR BIOLOGY REPORTER   33 ( 4 )   1075 - 1087   2015.8   ISSN:0735-9640 eISSN:1572-9818

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    Jatropha is known for its ability to grow in marginal lands and drought prone areas receiving limited amounts of rainfall. Accordingly, gene discovery in Jatropha will be useful for providing a source of genetic information for the improvement of drought tolerance in crops. In this study, gene expression profiling was performed using a newly developed Jatropha 44 K custom oligomicroarray on Jatropha plants subjected to drought stress and recovery from stress. When the gene expression patterns were compared between those differentially expressed during exposure to drought stress and re-watering, it was possible to identify 332 genes that are involved in the response to dehydration, while 585 genes were found to be significant during recovery, and 374 genes are associated with both dehydration and recovery. Furthermore, representative genes from the three gene categories were compared to those found in other plant species, and a basic understanding on how Jatropha copes with drought and its mechanism for survival in dry conditions is discussed. Taken together, the oligomicroarray that we developed in this study is a useful tool for analyzing expression profiles of Jatropha genes to better understand the molecular mechanism underlying drought stress responses as well as other aspects of molecular studies in Jatropha.

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  • A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly Reviewed International journal

    Hideki Nishikawa, Takuro Iijima, Rei Kajitani, Junichi Yamaguchi, Toshiya Ando, Yutaka Suzuki, Sumio Sugano, Asao Fujiyama, Shunichi Kosugi, Hideki Hirakawa, Satoshi Tabata, Katsuhisa Ozaki, Hiroya Morimoto, Kunio Ihara, Madoka Obara, Hiroshi Hori, Takehiko Itoh, Haruhiko Fujiwara

    NATURE GENETICS   47 ( 4 )   405 - U169   2015.4   ISSN:1061-4036 eISSN:1546-1718

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    In Batesian mimicry, animals avoid predation by resembling distasteful models. In the swallowtail butterfly Papilio polytes, only mimetic-form females resemble the unpalatable butterfly Pachliopta aristolochiae. A recent report showed that a single gene, doublesex (dsx), controls this mimicry(1); however, the detailed molecular mechanisms remain unclear. Here we determined two whole-genome sequences of P. polytes and a related species, Papilio xuthus, identifying a single similar to 130-kb autosomal inversion, including dsx, between mimetic (H-type) and non-mimetic (h-type) chromosomes in P. polytes. This inversion is associated with the mimicry-related locus H, as identified by linkage mapping. Knockdown experiments demonstrated that female-specific dsx isoforms expressed from the inverted H allele (dsx(H)) induce mimetic coloration patterns and simultaneously repress non-mimetic patterns. In contrast, dsx(h) does not alter mimetic patterns. We propose that dsx(H) switches the coloration of predetermined wing patterns and that female-limited polymorphism is tightly maintained by chromosomal inversion.

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  • Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don International journal

    Hideki Hirakawa, Yoshihiro Okada, Hiroaki Tabuchi, Kenta Shirasawa, Akiko Watanabe, Hisano Tsuruoka, Chiharu Minami, Shinobu Nakayama, Shigemi Sasamoto, Mitsuyo Kohara, Yoshie Kishida, Tsunakazu Fujishiro, Midori Kato, Keiko Nanri, Akiko Komaki, Masaru Yoshinaga, Yasuhiro Takahata, Masaru Tanaka, Satoshi Tabata, Sachiko N. Isobe

    DNA RESEARCH   22 ( 2 )   171 - 179   2015.4   ISSN:1340-2838 eISSN:1756-1663

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    Ipomoea trifida (H. B. K.) G. Don. is the most likely diploid ancestor of the hexaploid sweet potato, I. batatas (L.) Lam. To assist in analysis of the sweet potato genome, de novo whole-genome sequencing was performed with two lines of I. trifida, namely the selfed line Mx23Hm and the highly heterozygous line 0431-1, using the Illumina HiSeq platform. We classified the sequences thus obtained as either 'core candidates' (common to the two lines) or 'line specific'. The total lengths of the assembled sequences of Mx23Hm (ITR_r1.0) was 513 Mb, while that of 0431-1 (ITRk_r1.0) was 712 Mb. Of the assembled sequences, 240 Mb (Mx23Hm) and 353 Mb (0431-1) were classified into core candidate sequences. A total of 62,407 (62.4 Mb) and 109,449 (87.2 Mb) putative genes were identified, respectively, in the genomes of Mx23Hm and 0431-1, of which 11,823 were derived from core sequences of Mx23Hm, while 28,831 were from the core candidate sequence of 0431-1. There were a total of 1,464,173 single-nucleotide polymorphisms and 16,682 copy number variations (CNVs) in the two assembled genomic sequences (under the condition of log(2) ratio of > 1 and CNV size > 1,000 bases). The results presented here are expected to contribute to the progress of genomic and genetic studies of I. trifida, as well as studies of the sweet potato and the genus Ipomoea in general.

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  • A reference genetic linkage map of apomictic Hieracium species based on expressed markers derived from developing ovule transcripts International journal

    Kenta Shirasawa, Melanie L. Hand, Steven T. Henderson, Takashi Okada, Susan D. Johnson, Jennifer M. Taylor, Andrew Spriggs, Hayley Siddons, Hideki Hirakawa, Sachiko Isobe, Satoshi Tabata, Anna M. G. Koltunow

    ANNALS OF BOTANY   115 ( 4 )   567 - 580   2015.3   ISSN:0305-7364 eISSN:1095-8290

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    Background and Aims Apomixis in plants generates clonal progeny with a maternal genotype through asexual seed formation. Hieracium subgenus Pilosella (Asteraceae) contains polyploid, highly heterozygous apomictic and sexual species. Within apomictic Hieracium, dominant genetic loci independently regulate the qualitative developmental components of apomixis. In H. praealtum, LOSS OF APOMEIOSIS (LOA) enables formation of embryo sacs without meiosis and LOSS OF PARTHENOGENESIS (LOP) enables fertilization-independent seed formation. A locus required for fertilization-independent endosperm formation (AutE) has been identified in H. piloselloides. Additional quantitative loci appear to influence the penetrance of the qualitative loci, although the controlling genes remain unknown. This study aimed to develop the first genetic linkage maps for sexual and apomictic Hieracium species using simple sequence repeat (SSR) markers derived from expressed transcripts within the developing ovaries.Methods RNA from microdissected Hieracium ovule cell types and ovaries was sequenced and SSRs were identified. Two different F-1 mapping populations were created to overcome difficulties associated with genome complexity and asexual reproduction. SSR markers were analysed within each mapping population to generate draft linkage maps for apomictic and sexual Hieracium species.Key Results A collection of 14 684 Hieracium expressed SSR markers were developed and linkage maps were constructed for Hieracium species using a subset of the SSR markers. Both the LOA and LOP loci were successfully assigned to linkage groups; however, AutE could not be mapped using the current populations. Comparisons with lettuce (Lactuca sativa) revealed partial macrosynteny between the two Asteraceae species.Conclusions A collection of SSR markers and draft linkage maps were developed for two apomictic and one sexual Hieracium species. These maps will support cloning of controlling genes at LOA and LOP loci in Hieracium and should also assist with identification of quantitative loci that affect the expressivity of apomixis. Future work will focus on mapping AutE using alternative populations.

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  • Complete nucleotide sequence of the IncN plasmid encoding IMP-6 and CTX-M-2 from emerging carbapenem-resistant Enterobacteriaceae in Japan. International journal

    Shizuo Kayama, Norifumi Shigemoto, Ryuichi Kuwahara, Kenshiro Oshima, Hideki Hirakawa, Junzo Hisatsune, Thomas Jové, Hisaaki Nishio, Katsutoshi Yamasaki, Yasunao Wada, Takeshi Ueshimo, Tetsuya Miura, Taijiro Sueda, Makoto Onodera, Michiya Yokozaki, Masahira Hattori, Hiroki Ohge, Motoyuki Sugai

    Antimicrobial agents and chemotherapy   59 ( 2 )   1356 - 1359   2015.2   ISSN:0066-4804 eISSN:1098-6596

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    We have determined the DNA sequence of Klebsiella pneumoniae multidrug resistance plasmid pKPI-6, which is a self-transmissible IncN-type plasmid. pKPI-6 harboring blaIMP-6 and blaCTX-M-2 confers a stealth-type carbapenem resistance phenotype on members of the family Enterobacteriaceae that is not detectable with imipenem. pKPI-6 is already epidemic in Japan, favoring the dissemination of IMP-6 and CTX-M-2 in members of the family Enterobacteriaceae.

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  • 日和見病原性細菌Asaia bogorensisのゲノムとRNA配列分析から明らかになった適応応答(Genome and RNA-seq analyses reveal adaptive responses of opportunistic pathogen Asaia bogorensis)

    河合 幹彦, 東 慶直, 東裏 典枝, 平川 英樹, 武部 聡, 松下 一信

    日本細菌学雑誌   70 ( 1 )   177 - 177   2015.2   ISSN:0021-4930 eISSN:1882-4110

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  • Clustering of CARMA1 through SH3-GUK domain interactions is required for its activation of NF-κB signalling. International journal

    Hiromitsu Hara, Tadashi Yokosuka, Hideki Hirakawa, Chitose Ishihara, Shinsuke Yasukawa, Masanori Yamazaki, Haruhiko Koseki, Hiroki Yoshida, Takashi Saito

    Nature communications   6   5555 - 5555   2015.1   ISSN:2041-1723

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    CARMA1-mediated NF-κB activation controls lymphocyte activation through antigen receptors and survival of some malignant lymphomas. CARMA1 clusters are formed on physiological receptor-mediated activation or by its oncogenic mutation in activated B-cell-diffuse large B-cell lymphomas (ABC-DLBCLs) with constitutive NF-κB activation. However, regulatory mechanisms and relevance of CARMA1 clusters in the NF-κB pathway are unclear. Here we show that SH3 and GUK domain interactions of CARMA1 link CARMA1 clustering to signal activation. SH3 and GUK domains of CARMA1 interact by either intra- or intermolecular mechanisms, which are required for activation-induced assembly of CARMA1. Disruption of these interactions abolishes the formation of CARMA1 microclusters at the immunological synapse, CARMA-regulated signal activation following antigen receptor stimulation as well as spontaneous CARMA1 clustering and NF-κB activation by the oncogenic CARMA1 mutation in ABC-DLBCLs. Thus, the SH3-GUK interactions that regulate CARMA1 cluster formations are promising therapeutic targets for ABC-DLBCLs.

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  • Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum) Reviewed

    Hikaru Tsukazaki, Shigenori Yaguchi, Shusei Sato, Hideki Hirakawa, Yuichi Katayose, Hiroyuki Kanamori, Kanako Kurita, Takeshi Itoh, Masahiko Kumagai, Satoshi Mizuno, Masao Hamada, Hiroyuki Fukuoka, Ken-ichiro Yamashita, John A. McCallum, Masayoshi Shigyo, Tadayuki Wako

    MOLECULAR BREEDING   35 ( 1 )   2015.1   ISSN:1380-3743 eISSN:1572-9788

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    Bunching onion (Allium fistulosum L.) is one of the most important vegetables in Japan. Although expressed sequence tag (EST)-derived markers for bulb onion (A. cepa L.) have been developed from medium-scale sequencing, comparable EST sequences in bunching onion are lacking. In this study, we obtained 54,903 bunching onion unigenes using transcriptome shotgun assembly (TSA) and two next-generation sequencing technologies, GS-FLX and HiSeq 2000. When bunching onion and bulb onion unigenes were compared, 10,688 were estimated as reciprocal best-hit relationships. In the bunching onion TSA sequences, we discovered 2,396 di- to pentanucleotide simple sequence repeat (SSR) motifs and 5,505 exon-intron boundary sites. Moreover, we detected 9,002 single nucleotide polymorphisms and 4,335 insertion-deletion (InDel) by comparing sequence reads obtained from two inbred lines, "F" and "A." TSA-derived SSR, cleaved amplified polymorphic sequences, InDels and intron-spanning markers were used to develop a linkage map. The genetic map, designated the FA map, contained 17 linkage groups with 364 markers (190 bunching onion TSAs, 96 bunching onion genomic SSRs, 39 bulb onion ESTs and 4 other markers) and covered a distance of 1,150 cM.

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  • Draft genome sequence of eggplant (solanum melongena L.): The representative solanum species indigenous to the old world International journal

    Hideki Hirakawa, Kenta Shirasawa, Koji Miyatake, Tsukasa Nunome, Satomi Negoro, Akio Ohyama, Hirotaka Yamaguchi, Shusei Sato, Sachiko Isobe, Satoshi Tabata, Hiroyuki Fukuoka

    DNA Research   21 ( 6 )   649 - 660   2014.12   ISSN:1340-2838 eISSN:1756-1663

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    © 2014 The Author. Unlike other important Solanaceae crops such as tomato, potato, chili pepper, and tobacco, all of which originated in South America and are cultivated worldwide, eggplant (Solanum melongena L.) is indigenous to the Old World and in this respect it is phylogenetically unique. To broaden our knowledge of the genomic nature of solanaceous plants further, we dissected the eggplant genome and built a draft genome dataset with 33,873 scaffolds termed SME-r2.5.1 that covers 833.1 Mb, ca. 74% of the eggplant genome. Approximately 90% of the gene space was estimated to be covered by SME-r2.5.1 and 85,446 genes were predicted in the genome. Clustering analysis of the predicted genes of eggplant along with the genes of three other solanaceous plants as well as Arabidopsis thaliana revealed that, of the 35,000 clusters generated, 4,018 were exclusively composed of eggplant genes that would perhaps confer eggplant-specific traits. Between eggplant and tomato, 16,573 pairs of genes were deduced to be orthologous, and 9,489 eggplant scaffolds could be mapped onto the tomato genome. Furthermore, 56 conserved synteny blocks were identified between the two species. The detailed comparative analysis of the eggplant and tomato genomes will facilitate our understanding of the genomic architecture of solanaceous plants, which will contribute to cultivation and further utilization of these crops.

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  • Metagenomic studies of activate sludge to search for genes and genomes with environmental and industrial importance

    Abe, T; Nakata, T; Kumagai, Y; Sato, S; Hirakawa, H; Kondo, A; Sugimoto, C; Ikemura, T; Matsui, K

    GENES & GENETIC SYSTEMS   89 ( 6 )   328 - 328   2014.12   ISSN:1341-7568 eISSN:1880-5779

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  • NODULE INCEPTION creates a long-distance negative feedback loop involved in homeostatic regulation of nodule organ production Reviewed International journal

    Takashi Soyano, Hideki Hirakawa, Shusei Sato, Makoto Hayashi, Masayoshi Kawaguchi

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   111 ( 40 )   14607 - 14612   2014.10   ISSN:0027-8424

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    Autoregulatory negative-feedback loops play important roles in fine-balancing tissue and organ development. Such loops are composed of short-range intercellular signaling pathways via cell-cell communications. On the other hand, leguminous plants use a long-distance negative-feedback system involving root-shoot communication to control the number of root nodules, root lateral organs that harbor symbiotic nitrogen-fixing bacteria known as rhizobia. This feedback system, known as autoregulation of nodulation (AON), consists of two long-distance mobile signals: root-derived and shoot-derived signals. Two Lotus japonicus CLAVATA3/ENDOSPERM SURROUNDING REGION (CLE)-related small peptides, CLE ROOT SIGNAL1 (CLE-RS1) and CLE-RS2, function as root-derived signals and are perceived by a shoot-acting AON factor, the HYPERNODULATION ABERRANT ROOT FORMATION1 (HAR1) receptor protein, an ortholog of Arabidopsis CLAVATA1, which is responsible for shoot apical meristem homeostasis. This peptide-receptor interaction is necessary for systemic suppression of nodulation. How the onset of nodulation activates AON and how optimal nodule numbers are maintained remain unknown, however. Here we show that an RWP-RK-containing transcription factor, NODULE INCEPTION (NIN), which induces nodule-like structures without rhizobial infection when expressed ectopically, directly targets CLE-RS1 and CLE-RS2. Roots constitutively expressing NIN systemically repress activation of endogenous NIN expression in untransformed roots of the same plant in a HAR1-dependent manner, leading to systemic suppression of nodulation and down-regulation of CLE expression. Our findings provide, to our knowledge, the first molecular evidence of a long-distance autoregulatory negative-feedback loop that homeostatically regulates nodule organ formation.

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    Other Link: http://orcid.org/0000-0002-0620-6734

  • Draft Sequences of the Radish (Raphanus sativus L.) Genome Reviewed International journal

    Hiroyasu Kitashiba, Feng Li, Hideki Hirakawa, Takahiro Kawanabe, Zhongwei Zou, Yoichi Hasegawa, Kaoru Tonosaki, Sachiko Shirasawa, Aki Fukushima, Shuji Yokoi, Yoshihito Takahata, Tomohiro Kakizaki, Masahiko Ishida, Shunsuke Okamoto, Koji Sakamoto, Kenta Shirasawa, Satoshi Tabata, Takeshi Nishio

    DNA RESEARCH   21 ( 5 )   481 - 490   2014.10   ISSN:1340-2838 eISSN:1756-1663

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    Radish (Raphanus sativus L., n = 5 9) is one of the major vegetables in Asia. Since the genomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) for a radish inbred line, and 76,592 scaffolds of &gt;= 300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified.

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  • Replacement of a terminal cytochrome c oxidase by ubiquinol oxidase during the evolution of acetic acid bacteria International journal

    Minenosuke Matsutani, Kota Fukushima, Chiho Kayama, Misato Arimitsu, Hideki Hirakawa, Hirohide Toyama, Osao Adachi, Toshiharu Yakushi, Kazunobu Matsushita

    BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS   1837 ( 10 )   1810 - 1820   2014.10   ISSN:0005-2728 eISSN:1879-2650

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    The bacterial aerobic respiratory chain has a terminal oxidase of the heme-copper oxidase superfamily, comprised of cytochrome c oxidase (COX) and ubiquinol oxidase (UOX); UOX evolved from COX. Acetobacter pasteurianus, an alpha-Proteobacterial acetic acid bacterium (AAB), produces UOX but not COX, although it has a partial COX gene cluster, ctaBD and ctaA, in addition to the UOX operon cyaBACD. We expressed ctaB and ctaA genes of A. pasteurianus in Escherichia coli and demonstrated their function as heme O and heme A synthases. We also found that the absence of ctaD function is likely due to accumulated mutations. These COX genes are closely related to other alpha-Proteobacterial COX proteins. However, the UOX operons of AAB are closely related to those of the beta/gamma-Proteobacteria (gamma-type UOX), distinct from the alpha/beta-Proteobacterial proteins (alpha-type UOX), but different from the other gamma-type UOX proteins by the absence of the cyoE heme O synthase. Thus, we suggest that A. pasteurianus has a functional gamma-type UOX but has lost the COX genes, with the exception of ctaB and ctaA, which supply the heme O and A moieties for UOX. Our results suggest that, in MB, COX was replaced by beta/gamma-Proteobacterial UOX via horizontal gene transfer, while the COX genes, except for the heme O/A synthase genes, were lost (C) 2014 Elsevier B.V. All rights reserved.

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  • Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.

    Shirasawa K, Isobe S, Tabata S, Hirakawa H

    Breeding science   64 ( 3 )   264 - 71   2014.9   ISSN:1344-7610

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  • Detection of genome donor species of neglected tetraploid crop Vigna reflexo-pilosa (créole bean), and genetic structure of diploid species based on newly developed EST-SSR markers from azuki bean (Vigna angularis) International journal

    Sompong Chankaew, Takehisa Isemura, Sachiko Isobe, Akito Kaga, Norihiko Tomooka, Prakit Somta, Hideki Hirakawa, Kenta Shirasawa, Duncan A. Vaughan, Peerasak Srinives

    PLoS ONE   9 ( 8 )   e104990   2014.8   ISSN:1932-6203 eISSN:1932-6203

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    Vigna reflexo-pilosa, which includes a neglected crop, is the only one tetraploid species in genus Vigna. The ancestral species that make up this allotetraploid species have not conclusively been identified, although previous studies suggested that a donor genome of V. reflexo-pilosa is V. trinervia. In this study, 1,429 azuki bean EST-SSR markers were developed of which 38 EST-SSR primer pairs that amplified one product in diploid species and two discrete products in tetraploid species were selected to analyze 268 accessions from eight taxa of seven Asian Vigna species including V. reflexo-pilosa var. glabra , V. reflexo-pilosa var. reflexo-pilosa, V. exilis, V. hirtella, V. minima, V. radiata var. sublobata, V. tenuicaulis and V. trinervia to identify genome donor of V. reflexo-pilosa. Since both diploid and tetraploid species were analyzed and each SSR primer pair detected two loci in the tetraploid species, we separated genomes of the tetraploid species into two different diploid types, viz. A and B. In total, 445 alleles were detected by 38 EST-SSR markers. The highest gene diversity was observed in V. hirtella. By assigning the discrete PCR products of V. reflexo-pilosa into two distinguished genomes, we were able to identify the two genome donor parents of créole bean. Phylogenetic and principal coordinate analyses suggested that V. hirtella is a species complex and may be composed of at least three distinct taxa. Both analyses also clearly demonstrated that V. trinervia and one taxon of V. hirtella are the genome donors of V. reflexo-pilosa. Gene diversity indicates that the evolution rate of ESTSSRs on genome B of créole bean might be faster than that on genome A. Species relationship among the Vigna species in relation to genetic data, morphology and geographical distribution are presented. © 2014 Chankaew et al.

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  • Identification of the carotenoid modifying gene PALE YELLOW PETAL 1 as an essential factor in xanthophyll esterification and yellow flower pigmentation in tomato (Solanum lycopersicum). Reviewed International journal

    Tohru Ariizumi, Sanae Kishimoto, Ryo Kakami, Takashi Maoka, Hideki Hirakawa, Yutaka Suzuki, Yuko Ozeki, Kenta Shirasawa, Stephane Bernillon, Yoshihiro Okabe, Annick Moing, Erika Asamizu, Christophe Rothan, Akemi Ohmiya, Hiroshi Ezura

    The Plant journal : for cell and molecular biology   79 ( 3 )   453 - 465   2014.8   ISSN:0960-7412 eISSN:1365-313X

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    Xanthophylls, the pigments responsible for yellow to red coloration, are naturally occurring carotenoid compounds in many colored tissues of plants. These pigments are esterified within the chromoplast; however, little is known about the mechanisms underlying their accumulation in flower organs. In this study, we characterized two allelic tomato (Solanum lycopersicum L.) mutants, pale yellow petal (pyp) 1-1 and pyp1-2, that have reduced yellow color intensity in the petals and anthers due to loss-of-function mutations. Carotenoid analyses showed that the yellow flower organs of wild-type tomato contained high levels of xanthophylls that largely consisted of neoxanthin and violaxanthin esterified with myristic and/or palmitic acids. Functional disruption of PYP1 resulted in loss of xanthophyll esters, which was associated with a reduction in the total carotenoid content and disruption of normal chromoplast development. These findings suggest that xanthophyll esterification promotes the sequestration of carotenoids in the chromoplast and that accumulation of these esters is important for normal chromoplast development. Next-generation sequencing coupled with map-based positional cloning identified the mutant alleles responsible for the pyp1 phenotype. PYP1 most likely encodes a carotenoid modifying protein that plays a vital role in the production of xanthophyll esters in tomato anthers and petals. Our results provide insight into the molecular mechanism underlying the production of xanthophyll esters in higher plants, thereby shedding light on a longstanding mystery.

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  • Identification of tightly linked SSR markers for flower type in carnation (Dianthus caryophyllus L.)

    Masafumi Yagi, Toshiya Yamamoto, Sachiko Isobe, Satoshi Tabata, Hideki Hirakawa, Hiroyasu Yamaguchi, Koji Tanase, Takashi Onozaki

    EUPHYTICA   198 ( 2 )   175 - 183   2014.7   ISSN:0014-2336 eISSN:1573-5060

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    Single or double flower type is one of the most important breeding targets in carnation (Dianthus caryophyllus L.). We mapped the D (85) locus, which controls flower type, to LG 85P_15-2 using a simple sequence repeat (SSR)-based genetic linkage map constructed using 91 F-2 progeny derived from a cross between line 85-11 (double flower) and 'Pretty Favvare' (single flower). A positional comparison using SSR markers as anchor loci revealed that the map positions of the D (85) locus corresponded to the single locus controlling the single flower type derived from wild D. capitatus ssp. andrzejowskianus. We identified four co-segregating SSR markers on the D (85) locus. Verification of the SSR markers in commercial cultivars revealed that two of the four SSR markers (CES0212 and CES1982) were tightly linked to the D (85) locus, and amplified a 176-bp and 269-bp allele, respectively, which were common and unique to double flower cultivars. The map positions of the D (85) locus and the tightly linked SSR markers will be useful for determining the genetic basis of flower type and for marker-assisted breeding of carnations.

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  • Mariner-based transposon mutagenesis for Bacteroides species. International journal

    Minoru Ichimura, Keiko Uchida, Haruyuki Nakayama-Imaohji, Hideki Hirakawa, Tomoyo Tada, Hidetoshi Morita, Koji Yasutomo, Katsuichiro Okazaki, Tomomi Kuwahara

    Journal of basic microbiology   54 ( 6 )   558 - 567   2014.6   ISSN:0233-111X eISSN:1521-4028

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    Bacteroides is one of the most predominant groups of human gut microbiota. Recent metagenomic analyses and studies on gnotobiotic mice demonstrated the tight association of Bacteroides with epithelial function, the gut immune system and systemic metabolism in the host. The mariner family transposon shows relatively low target site specificity and has hosts ranging from prokaryotes to eukaryotes. Thereby, random mutagenesis using the mariner family transposon is expected to identify key molecules for human-Bacteroides symbiosis. In this study, we constructed the plasmid pMI07 to deliver the gene cassette (ermF/ITR), which harbors the erythromycin resistant marker (ermF) and the inverted repeat sequences (ITRs) recognized by Himar1 transposase, to Bacteroides via electrotransformation. pMI07 successfully delivered ermF/ITR to the Bacteroides genomes and generated thousands of insertion mutants/μg of pMI07 in B. thetaiotaomicron, B. fragilis, B. ovatus, and also, although to a lesser extent, B. vulgatus. Analyses of the ermF/ITR insertion sites in B. thetaiotaomicron and B. vulgatus revealed that the cassette targeted the dinucleotide TA and integrated into the genomes in an unbiased manner. The data reported here will provide useful information for transposon mutagenesis in Bacteroides species, which will enable identification of the genes responsible for their unique phenotypes.

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  • Endoreduplication-mediated initiation of symbiotic organ development in Lotus japonicus International journal

    Takuya Suzaki, Momoyo Ito, Emiko Yoro, Shusei Sato, Hideki Hirakawa, Naoya Takeda, Masayoshi Kawaguchi

    DEVELOPMENT   141 ( 12 )   2441 - 2445   2014.6   ISSN:0950-1991 eISSN:1477-9129

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    Many leguminous plants have a unique ability to reset and alter the fate of differentiated root cortical cells to form new organs of nitrogen-fixing root nodules during legume-Rhizobium symbiosis. Recent genetic studies on the role of cytokinin signaling reveal that activation of cytokinin signaling is crucial to the nodule organogenesis process. However, the genetic mechanism underlying the initiation of nodule organogenesis is poorly understood due to the low number of genes that have been identified. Here, we have identified a novel nodulation-deficient mutant named vagrant infection thread 1 (vag1) after suppressor mutant screening of spontaneous nodule formation 2, a cytokinin receptor gain-of-function mutant in Lotus japonicus. The VAG1 gene encodes a protein that is putatively orthologous to Arabidopsis ROOT HAIRLESS 1/HYPOCOTYL 7, a component of the plant DNA topoisomerase VI that is involved in the control of endoreduplication. Nodule phenotype of the vag1 mutant shows that VAG1 is required for the ploidy-dependent cell growth of rhizobial-infected cells. Furthermore, VAG1 mediates the onset of endoreduplication in cortical cells during early nodule development, which may be essential for the initiation of cortical cell proliferation that leads to nodule primordium formation. In addition, cortical infection is severely impaired in the vag1 mutants, whereas the epidermal infection threads formation is normal. This suggests that the VAG1-mediated endoreduplication of cortical cells may be required for the guidance of symbiotic bacteria to host meristematic cells.

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  • Sequence analysis of the genome of carnation (Dianthus caryophyllus L.) International journal

    Masafumi Yagi, Shunichi Kosugi, Hideki Hirakawa, Akemi Ohmiya, Koji Tanase, Taro Harada, Kyutaro Kishimoto, Masayoshi Nakayama, Kazuo Ichimura, Takashi Onozaki, Hiroyasu Yamaguchi, Nobuhiro Sasaki, Taira Miyahara, Yuzo Nishizaki, Yoshihiro Ozeki, Noriko Nakamura, Takamasa Suzuki, Yoshikazu Tanaka, Shusei Sato, Kenta Shirasawa, Sachiko Isobe, Yoshinori Miyamura, Akiko Watanabe, Shinobu Nakayama, Yoshie Kishida, Mitsuyo Kohara, Satoshi Tabata

    DNA Research   21 ( 3 )   231 - 241   2014.6   ISSN:1340-2838 eISSN:1756-1663

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    The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. 'Francesco' was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568 887 315 bp, consisting of 45 088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16 644 bp and 60 737 bp, respectively, and the longest scaffold was 1 287 144 bp. The average GC content of the contig sequences was 36%. A total of 1050, 13, 92 and 143 genes for tRNAs, rRNAs, snoRNA and miRNA, respectively, were identified in the assembled genomic sequences. For protein-encoding genes, 43 266 complete and partial gene structures excluding those in transposable elements were deduced. Gene coverage was ∼98%, as deduced from the coverage of the core eukaryotic genes. Intensive characterization of the assigned carnation genes and comparison with those of other plant species revealed characteristic features of the carnation genome. The results of this study will serve as a valuable resource for fundamental and applied research of carnation, especially for breeding new carnation varieties. Further information on the genomic sequences is available at http://carnation.kazusa.or.jp. © 2013 The Author.

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  • The rice endosperm ADP-glucose pyrophosphorylase large subunit is essential for optimal catalysis and allosteric regulation of the heterotetrameric enzyme.

    Aytug Tuncel, Joe Kawaguchi, Yasuharu Ihara, Hiroaki Matsusaka, Aiko Nishi, Tetsuhiro Nakamura, Satoru Kuhara, Hideki Hirakawa, Yasunori Nakamura, Bilal Cakir, Ai Nagamine, Thomas W Okita, Seon-Kap Hwang, Hikaru Satoh

    Plant & cell physiology   55 ( 6 )   1169 - 1183   2014.6   ISSN:0032-0781 eISSN:1471-9053

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    Although an alternative pathway has been suggested, the prevailing view is that starch synthesis in cereal endosperm is controlled by the activity of the cytosolic isoform of ADPglucose pyrophosphorylase (AGPase). In rice, the cytosolic AGPase isoform is encoded by the OsAGPS2b and OsAGPL2 genes, which code for the small (S2b) and large (L2) subunits of the heterotetrameric enzyme, respectively. In this study, we isolated several allelic missense and nonsense OsAGPL2 mutants by N-methyl-N-nitrosourea (MNU) treatment of fertilized egg cells and by TILLING (Targeting Induced Local Lesions in Genomes). Interestingly, seeds from three of the missense mutants (two containing T139I and A171V) were severely shriveled and had seed weight and starch content comparable with the shriveled seeds from OsAGPL2 null mutants. Results from kinetic analysis of the purified recombinant enzymes revealed that the catalytic and allosteric regulatory properties of these mutant enzymes were significantly impaired. The missense heterotetramer enzymes and the S2b homotetramer had lower specific (catalytic) activities and affinities for the activator 3-phosphoglycerate (3-PGA). The missense heterotetramer enzymes showed more sensitivity to inhibition by the inhibitor inorganic phosphate (Pi) than the wild-type AGPase, while the S2b homotetramer was profoundly tolerant to Pi inhibition. Thus, our results provide definitive evidence that starch biosynthesis during rice endosperm development is controlled predominantly by the catalytic activity of the cytoplasmic AGPase and its allosteric regulation by the effectors. Moreover, our results show that the L2 subunit is essential for both catalysis and allosteric regulatory properties of the heterotetramer enzyme.

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  • Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species International journal

    Hideki Hirakawa, Kenta Shirasawa, Shunichi Kosugi, Kosuke Tashiro, Shinobu Nakayama, Manabu Yamada, Mistuyo Kohara, Akiko Watanabe, Yoshie Kishida, Tsunakazu Fujishiro, Hisano Tsuruoka, Chiharu Minami, Shigemi Sasamoto, Midori Kato, Keiko Nanri, Akiko Komaki, Tomohiro Yanagi, Qin Guoxin, Fumi Maeda, Masami Ishikawa, Satoru Kuhara, Shusei Sato, Satoshi Tabata, Sachiko N. Isobe

    DNA RESEARCH   21 ( 2 )   169 - 181   2014.4   ISSN:1340-2838 eISSN:1756-1663

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    Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this octoploid genome through comparison with its wild relatives, F. iinumae, F. nipponica, F. nubicola, and F. orientalis by de novo whole-genome sequencing on an Illumina and Roche 454 platforms. The total length of the assembled Illumina genome sequences obtained was 698 Mb for F. x ananassa, and similar to 200 Mb each for the four wild species. Subsequently, a virtual reference genome termed FANhybrid_r1.2 was constructed by integrating the sequences of the four homoeologous subgenomes of F. x ananassa, from which heterozygous regions in the Roche 454 and Illumina genome sequences were eliminated. The total length of FANhybrid_r1.2 thus created was 173.2 Mb with the N50 length of 5137 bp. The Illumina-assembled genome sequences of F. x ananassa and the four wild species were then mapped onto the reference genome, along with the previously published F. vesca genome sequence to establish the subgenomic structure of F. x ananassa. The strategy adopted in this study has turned out to be successful in dissecting the genome of octoploid F. x ananassa and appears promising when applied to the analysis of other polyploid plant species.

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  • Draft genomic DNA sequence of the facultatively methylotrophic bacterium Acidomonas methanolica type strain MB58 International journal

    Norie Higashiura, Hiromi Hadano, Hideki Hirakawa, Minenosuke Matsutani, So Takebe, Kazunobu Matsushita, Yoshinao Azuma

    FEMS MICROBIOLOGY LETTERS   351 ( 1 )   9 - 13   2014.2   ISSN:0378-1097 eISSN:1574-6968

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    Acidomonas methanolica (former name: Acetobacter methanolicus) is a unique acetic acid bacterium capable of growing on methanol as a sole carbon source. We reported the draft genome sequencing of A.methanolica type strain MB58, showing that it contains 3270 protein-coding genes, including the genes involved in oxidation of methanol, such as mxaFJGIRSACKL and hxlAB, and oxidation of ethanol, such as adhAB and adhS.

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  • Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases. Reviewed

    Erika Asamizu, Hisako Ichihara, Akihiro Nakaya, Yasukazu Nakamura, Hideki Hirakawa, Takahiro Ishii, Takuro Tamura, Kaoru Fukami-Kobayashi, Yukari Nakajima, Satoshi Tabata

    Plant & cell physiology   55 ( 1 )   e8   2014.1   ISSN:0032-0781 eISSN:1471-9053

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    The Plant Genome DataBase Japan (PGDBj, http://pgdbj.jp/?ln=en) is a portal website that aims to integrate plant genome-related information from databases (DBs) and the literature. The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search over the contents of the DBs. The three DBs are as follows. (i) The Ortholog DB, providing gene cluster information based on the amino acid sequence similarity. Over 500,000 amino acid sequences of 20 Viridiplantae species were subjected to reciprocal BLAST searches and clustered. Sequences from plant genome DBs (e.g. TAIR10 and RAP-DB) were also included in the cluster with a direct link to the original DB. (ii) The Plant Resource DB, integrating the SABRE DB, which provides cDNA and genome sequence resources accumulated and maintained in the RIKEN BioResource Center and National BioResource Projects. (iii) The DNA Marker DB, providing manually or automatically curated information of DNA markers, quantitative trait loci and related linkage maps, from the literature and external DBs. As the PGDBj targets various plant species, including model plants, algae, and crops important as food, fodder and biofuel, researchers in the field of basic biology as well as a wide range of agronomic fields are encouraged to perform searches using DNA sequences, gene names, traits and phenotypes of interest. The PGDBj will return the search results from the component DBs and various types of linked external DBs.

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  • Development of EST-SSR markers and construction of a linkage map in faba bean (<i>Vicia faba</i>)

    El-Rodeny Walid, Kimura Mitsuhiro, Hirakawa Hideki, Sabah Attia, Shirasawa Kenta, Sato Shusei, Tabata Satoshi, Sasamoto Shigemi, Watanabe Akiko, Kawashima Kumiko, Kato Midori, Wada Tsuyuko, Tsuruoka Hisano, Takahashi Chika, Minami Chiharu, Nanri Keiko, Nakayama Shinobu, Kohara Mitsuyo, Yamada Manabu, Kishida Yoshie, Fujishiro Tsunakazu, Isobe Sachiko

    Breeding Science   64 ( 3 )   252 - 263   2014   ISSN:13447610 eISSN:13473735

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    To develop a high density linkage map in faba bean, a total of 1,363 FBES (<u>F</u>aba <u>b</u>ean <u>e</u>xpressed sequence tag [EST]-derived <u>s</u>imple sequence repeat [SSR]) markers were designed based on 5,090 non-redundant ESTs developed in this study. A total of 109 plants of a ‘Nubaria 2’ × ‘Misr 3’ F<sub>2</sub> mapping population were used for map construction. Because the parents were not pure homozygous lines, the 109 F<sub>2</sub> plants were divided into three subpopulations according to the original F<sub>1</sub> plants. Linkage groups (LGs) generated in each subpopulation were integrated by commonly mapped markers. The integrated ‘Nubaria 2’ × ‘Misr 3’ map consisted of six LGs, representing a total length of 684.7 cM, with 552 loci. Of the mapped loci, 47% were generated from multi-loci diagnostic (MLD) markers. Alignment of homologous sequence pairs along each linkage group revealed obvious syntenic relationships between LGs in faba bean and the genomes of two model legumes, <i>Lotus japonicus</i> and <i>Medicago truncatula</i>. In a polymorphic analysis with ten Egyptian faba bean varieties, 78.9% (384/487) of the FBES markers showed polymorphisms. Along with the EST-SSR markers, the dense map developed in this study is expected to accelerate marker assisted breeding in faba bean.

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  • Legume and <i>Lotus japonicus</i> Databases

    Hirakawa, H; Mun, T; Sato, S; Andersen, SU

    LOTUS JAPONICUS GENOME   259 - 267   2014   ISSN:2199-4781 ISBN:978-3-662-44269-2

  • Transcriptomic profiles of nodule senescence in <i>Lotus japonicus</i> and <i>Mesorhizobium loti</i> symbiosis

    Chungopast Sirinapa, Hirakawa Hideki, Sato Shusei, Handa Yoshihiro, Saito Katsuharu, Kawaguchi Masayoshi, Tajima Shigeyuki, Nomura Mika

    Plant Biotechnology   31 ( 4 )   345 - 349   2014   ISSN:13424580 eISSN:13476114

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    Nodule senescence is a complex developmental process during which essential nutrients are recycled. In order to understand the regulatory mechanism, transcript-profiling analysis during nodule senescence was performed in the <i>Lotus japonicus</i>-<i>Mesorhizobium loti</i> symbiosis. Microarray data showed significantly up-regulated expressions in 641 genes out of a total of 20,165 genes during nodule senescence, and down-regulated expressions were observed in 416 genes. These up-regulated genes during senescence were related to cell wall/membrane/envelope biogenesis and extracellular structures. Down-regulated genes were mainly responsible for defense mechanisms. We classified senescence up-regulated genes in two clusters. Genes in cluster 1 were induced at senescence specific stage and those in cluster 2 were induced from nitrogen fixation stage and expressed until nodule senescence. The genes in cluster 1 included typical marker for senescence like gene for heat shock protein. Four hundred sixteen down-regulated genes during nodule senescence were also classified in two clusters, cluster 3 and cluster 4. These genes corresponded to metabolisms for amino acid and plant hormones which are necessary for growth and cell division during nodule development and nitrogen fixation. These results provide the comprehensive data source for investigation of molecular mechanisms underlying nodule senescence in <i>Lotus japonicus-Mesorhizobium loti</i> symbiosis.

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  • Emergence of Staphylococcus aureus carrying multiple drug resistance genes on a plasmid encoding exfoliative toxin B. International journal

    Junzo Hisatsune, Hideki Hirakawa, Takayuki Yamaguchi, Yasuyuki Fudaba, Kenshiro Oshima, Masahira Hattori, Fuminori Kato, Shizuo Kayama, Motoyuki Sugai

    Antimicrobial agents and chemotherapy   57 ( 12 )   6131 - 6140   2013.12   ISSN:0066-4804 eISSN:1098-6596

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    We report the complete nucleotide sequence and analysis of pETBTY825, a Staphylococcus aureus TY825 plasmid encoding exfoliative toxin B (ETB). S. aureus TY825 is a clinical isolate obtained from an impetigo patient in 2002. The size of pETBTY825, 60.6 kbp, was unexpectedly larger than that of the archetype pETBTY4 (∼30 kbp). Genomic comparison of the plasmids shows that pETBTY825 has the archetype pETBTY4 as the backbone and has a single large extra DNA region of 22.4 kbp. The extra DNA region contains genes for resistance to aminoglycoside [aac(6')/aph(2″)], macrolide (msrA), and penicillin (blaZ). A plasmid deletion experiment indicated that these three resistance elements were functionally active. We retrospectively examined the resistance profile of the clinical ETB-producing S. aureus strains isolated in 1977 to 2007 using a MIC determination with gentamicin (GM), arbekacin (ABK), and erythromycin (EM) and by PCR analyses for aac(6')/aph(2″) and msrA using purified plasmid preparations. The ETB-producing S. aureus strains began to display high resistance to GM, which was parallel with the detection of aac(6')/aph(2″) and mecA, after 1990. Conversely, there was no significant change in the ABK MIC during the testing period, although it had a tendency to slightly increase. After 2001, isolates resistant to EM significantly increased; however, msrA was hardly detected in ETB-producing S. aureus strains, and only five isolates were positive for both aac(6')/aph(2″) and msrA. In this study, we report the emergence of a fusion plasmid carrying the toxin gene etb and drug resistance genes. Prevalence of the pETBTY825 carrier may further increase the clinical threat, since ETB-producing S. aureus is closely related to more severe impetigo or staphylococcal scalded-skin syndrome (SSSS), which requires a general antimicrobial treatment.

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  • Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato International journal

    Kenta Shirasawa, Hiroyuki Fukuoka, Hiroshi Matsunaga, Yuhko Kobayashi, Issei Kobayashi, Hideki Hirakawa, Sachiko Isobe, Satoshi Tabata

    DNA Research   20 ( 6 )   593 - 603   2013.12   ISSN:1340-2838 eISSN:1756-1663

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    With the aim of understanding relationship between genetic and phenotypic variations in cultivated tomato, single nucleotide polymorphism (SNP) markers covering the whole genome of cultivated tomato were developed and genome-wide association studies (GWAS) were performed. The whole genomes of six tomato lines were sequenced with the ABI-5500xl SOLiD sequencer. Sequence reads covering ∼13.7× of the genome for each line were obtained, and mapped onto tomato reference genomes (SL2.40) to detect ∼1.5 million SNP candidates. Of the identified SNPs, 1.5% were considered to confer gene functions. In the subsequent Illumina GoldenGate assay for 1536 SNPs, 1293 SNPs were successfully genotyped, and 1248 showed polymorphisms among 663 tomato accessions. The whole-genome linkage disequilibrium (LD) analysis detected highly biased LD decays between euchromatic (58 kb) and heterochromatic regions (13.8 Mb). Subsequent GWAS identified SNPs that were significantly associated with agronomical traits, with SNP loci located near genes that were previously reported as candidates for these traits. This study demonstrates that attractive loci can be identified by performing GWAS with a large number of SNPs obtained from re-sequencing analysis. © The Author 2013.

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  • Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.) International journal

    Masafumi Yagi, Toshiya Yamamoto, Sachiko Isobe, Hideki Hirakawa, Satoshi Tabata, Koji Tanase, Hiroyasu Yamaguchi, Takashi Onozaki

    BMC GENOMICS   14   734 - 734   2013.10   ISSN:1471-2164

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    Background: Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F-2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research.Results: We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data.Conclusions: The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs.

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  • Complete genomic DNA sequence of the East Asian spotted fever disease agent Rickettsia japonica. Reviewed International journal

    Minenosuke Matsutani, Motohiko Ogawa, Naohisa Takaoka, Nozomu Hanaoka, Hidehiro Toh, Atsushi Yamashita, Kenshiro Oshima, Hideki Hirakawa, Satoru Kuhara, Harumi Suzuki, Masahira Hattori, Toshio Kishimoto, Shuji Ando, Yoshinao Azuma, Mutsunori Shirai

    PloS one   8 ( 9 )   e71861   2013.9   ISSN:1932-6203

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    Rickettsia japonica is an obligate intracellular alphaproteobacteria that causes tick-borne Japanese spotted fever, which has spread throughout East Asia. We determined the complete genomic DNA sequence of R. japonica type strain YH (VR-1363), which consists of 1,283,087 base pairs (bp) and 971 protein-coding genes. Comparison of the genomic DNA sequence of R. japonica with other rickettsiae in the public databases showed that 2 regions (4,323 and 216 bp) were conserved in a very narrow range of Rickettsia species, and the shorter one was inserted in, and disrupted, a preexisting open reading frame (ORF). While it is unknown how the DNA sequences were acquired in R. japonica genomes, it may be a useful signature for the diagnosis of Rickettsia species. Instead of the species-specific inserted DNA sequences, rickettsial genomes contain Rickettsia-specific palindromic elements (RPEs), which are also capable of locating in preexisting ORFs. Precise alignments of protein and DNA sequences involving RPEs showed that when a gene contains an inserted DNA sequence, each rickettsial ortholog carried an inserted DNA sequence at the same locus. The sequence, ATGAC, was shown to be highly frequent and thus characteristic in certain RPEs (RPE-4, RPE-6, and RPE-7). This finding implies that RPE-4, RPE-6, and RPE-7 were derived from a common inserted DNA sequence.

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  • Identification and characterization of a novel aac(6')-Iag associated with the blaIMP-1-integron in a multidrug-resistant Pseudomonas aeruginosa. International journal

    Kanao Kobayashi, Ikue Hayashi, Syuntaro Kouda, Fuminori Kato, Tamaki Fujiwara, Shizuo Kayama, Hideki Hirakawa, Hideyuki Itaha, Hiroki Ohge, Naomasa Gotoh, Tsuguru Usui, Akio Matsubara, Motoyuki Sugai

    PloS one   8 ( 8 )   e70557   2013.8   ISSN:1932-6203

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    In a continuing study from Dec 2006 to Apr 2008, we characterized nine multi-drug resistant Pseudomonas aeruginosa strains isolated from four patients in a ward at the Hiroshima University Hospital, Japan. Pulsed-field gel electrophoresis of SpeI-digested genomic DNAs from the isolates suggested the clonal expansion of a single strain; however, only one strain, NK0009, was found to produce metallo-β-lactamase. PCR and subsequent sequencing analysis indicated NK0009 possessed a novel class 1 integron, designated as In124, that carries an array of four gene cassettes: a novel aminoglycoside (AG) resistance gene, aac(6')-Iag, blaIMP-1, a truncated form of blaIMP-1, and a truncated form of aac(6')-Iag. The aac(6')-Iag encoded a 167-amino-acid protein that shows 40% identity with AAC(6')-Iz. Recombinant AAC(6')-Iag protein showed aminoglycoside 6'-N-acetyltransferase activity using thin-layer chromatography (TLC) and MS spectrometric analysis. Escherichia coli carrying aac(6')-Iag showed resistance to amikacin, arbekacin, dibekacin, isepamicin, kanamycin, sisomicin, and tobramycin; but not to gentamicin. A conjugation experiment and subsequent Southern hybridization with the gene probes for blaIMP-1 and aac(6')-Ig strongly suggested In124 is on a conjugal plasmid. Transconjugants acquired resistance to gentamicin and were resistant to virtually all AGs, suggesting that the In124 conjugal plasmid also possesses a gene conferring resistance to gentamicin.

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  • Effect of Kampo medicine "Dai-kenchu-to" on microbiome in the intestine of the rats with fast stress

    Yoshikawa, K; Shimada, M; Kuwahara, T; Hirakawa, H; Kurita, N; Sato, H; Utsunomiya, T; Iwata, T; Miyatani, T; Higashijima, J; Kashihara, H; Takasu, C; Matsumoto, N; Nakayama-Imaohji, H

    JOURNAL OF MEDICAL INVESTIGATION   60 ( 3-4 )   221 - 227   2013.8   ISSN:1343-1420 eISSN:1349-6867

  • Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna. International journal

    Yoji Nakamura, Kazuki Mori, Kenji Saitoh, Kenshiro Oshima, Miyuki Mekuchi, Takuma Sugaya, Yuya Shigenobu, Nobuhiko Ojima, Shigeru Muta, Atushi Fujiwara, Motoshige Yasuike, Ichiro Oohara, Hideki Hirakawa, Vishwajit Sur Chowdhury, Takanori Kobayashi, Kazuhiro Nakajima, Motohiko Sano, Tokio Wada, Kosuke Tashiro, Kazuho Ikeo, Masahira Hattori, Satoru Kuhara, Takashi Gojobori, Kiyoshi Inouye

    Proceedings of the National Academy of Sciences of the United States of America   110 ( 27 )   11061 - 11066   2013.7   ISSN:0027-8424 eISSN:1091-6490

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    Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (SWS2), rhodopsin (RH1), and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e., blue shift). Pacific bluefin tuna has at least five RH2 paralogs, the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover, phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus, Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1, RH2, and SWS2), which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and, thereby, could help to improve the technology to culture such fish in captivity for resource management.

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  • Genome-Wide SNP Genotyping to Infer the Effects on Gene Functions in Tomato International journal

    Hideki Hirakawa, Kenta Shirasawa, Akio Ohyama, Hiroyuki Fukuoka, Koh Aoki, Christophe Rothan, Shusei Sato, Sachiko Isobe, Satoshi Tabata

    DNA RESEARCH   20 ( 3 )   221 - 233   2013.6   ISSN:1340-2838 eISSN:1756-1663

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    The genotype data of 7054 single nucleotide polymorphism (SNP) loci in 40 tomato lines, including inbred lines, F-1 hybrids, and wild relatives, were collected using Illumina's Infinium and GoldenGate assay platforms, the latter of which was utilized in our previous study. The dendrogram based on the genotype data corresponded well to the breeding types of tomato and wild relatives. The SNPs were classified into six categories according to their positions in the genes predicted on the tomato genome sequence. The genes with SNPs were annotated by homology searches against the nucleotide and protein databases, as well as by domain searches, and they were classified into the functional categories defined by the NCBI's eukaryotic orthologous groups (KOG). To infer the SNPs' effects on the gene functions, the three-dimensional structures of the 843 proteins that were encoded by the genes with SNPs causing missense mutations were constructed by homology modelling, and 200 of these proteins were considered to carry non-synonymous amino acid substitutions in the predicted functional sites. The SNP information obtained in this study is available at the Kazusa Tomato Genomics Database (http://plant1.kazusa.or.jp/tomato/).

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  • Unique regulatory mechanism of sporulation and enterotoxin production in Clostridium perfringens. International journal

    Kaori Ohtani, Hideki Hirakawa, Daniel Paredes-Sabja, Kosuke Tashiro, Satoru Kuhara, Mahfuzur R Sarker, Tohru Shimizu

    Journal of bacteriology   195 ( 12 )   2931 - 2936   2013.6   ISSN:0021-9193

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    Clostridium perfringens causes gas gangrene and gastrointestinal (GI) diseases in humans. The most common cause of C. perfringens-associated food poisoning is the consumption of C. perfringens vegetative cells followed by sporulation and production of enterotoxin in the gut. Despite the importance of spore formation in C. perfringens pathogenesis, the details of the regulation of sporulation have not yet been defined fully. In this study, microarray and bioinformatic analyses identified a candidate gene (the RNA regulator virX) for the repression of genes encoding positive regulators (Spo0A and sigma factors) of C. perfringens sporulation. A virX mutant constructed in the food poisoning strain SM101 had a much higher sporulation efficiency than that of the wild type. The transcription of sigE, sigF, and sigK was strongly induced at 2.5 h of culture of the virX mutant. Moreover, the transcription of the enterotoxin gene was also strongly induced in the virX mutant. Western blotting confirmed that the levels of enterotoxin production were higher in the virX mutant than in the wild type. These observations indicated that the higher levels of sporulation and enterotoxin production in the virX mutant were specifically due to inactivation of the virX gene. Since virX homologues were not found in any Bacillus species but were present in other clostridial species, our findings identify further differences in the regulation of sporulation between Bacillus and certain Clostridium species. The virX RNA regulator plays a key role in the drastic shift in lifestyle of the anaerobic flesh eater C. perfringens between the vegetative state (for gas gangrene) and the sporulating state (for food poisoning).

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  • Genome structure of jatropha curcas L.

    Shusei Sato, Hideki Hirakawa, Suguru Tsuchimoto, Hiroe Sakai, Nakako Shibagaki, Sachihiro Matsunaga, Kiichi Fukui, Satoshi Tabata

    Jatropha, Challenges for a New Energy Crop   2   563 - 576   2013.5

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    The recent progress in DNA sequencing technology has allowed us to acquire information on the structures of whole genomes of various agronomically important plants in a relatively short period of time. In order to understand the genetic systems carried by Jatropha curcas and to accelerate the process of molecular breeding, comprehensive analyses of genes and the genome of this plant have been conducted using both conventional and advanced technologies, and a large quantity of sequence data has been accumulated. The latest draft sequence of the genome of J. curcas is 297 Mb long, and is presumed to cover 99 % of the gene space, with an average GC content of 33.8 %. By combining with the transcriptome information, a total of 30,203 protein-encoding genes, in addition to the 17,575 transposon-related genes and 2,124 putative pseudogenes, were assigned to the genome. Information on the genomic sequences and genes is available at http://www.kazusa.or.jp/jatropha/.

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  • Integrated Consensus Map of Cultivated Peanut and Wild Relatives Reveals Structures of the A and B Genomes of Arachis and Divergence of the Legume Genomes International journal

    Kenta Shirasawa, David J. Bertioli, Rajeev K. Varshney, Marcio C. Moretzsohn, Soraya C. M. Leal-Bertioli, Mahendar Thudi, Manish K. Pandey, Jean-Francois Rami, Daniel Fonceka, Makanahally V. C. Gowda, Hongde Qin, Baozhu Guo, Yanbin Hong, Xuanqiang Liang, Hideki Hirakawa, Satoshi Tabata, Sachiko Isobe

    DNA RESEARCH   20 ( 2 )   173 - 184   2013.4   ISSN:1340-2838 eISSN:1756-1663

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    The complex, tetraploid genome structure of peanut (Arachis hypogaea) has obstructed advances in genetics and genomics in the species. The aim of this study is to understand the genome structure of Arachis by developing a high-density integrated consensus map. Three recombinant inbred line populations derived from crosses between the A genome diploid species, Arachis duranensis and Arachis stenosperma; the B genome diploid species, Arachis ipaensis and Arachis magna; and between the AB genome tetraploids, A. hypogaea and an artificial amphidiploid (A. ipaensis x A. duranensis)(4x), were used to construct genetic linkage maps: 10 linkage groups (LGs) of 544 cM with 597 loci for the A genome; 10 LGs of 461 cM with 798 loci for the B genome; and 20 LGs of 1442 cM with 1469 loci for the AB genome. The resultant maps plus 13 published maps were integrated into a consensus map covering 2651 cM with 3693 marker loci which was anchored to 20 consensus LGs corresponding to the A and B genomes. The comparative genomics with genome sequences of Cajanus cajan, Glycine max, Lotus japonicas, and Medicago truncatula revealed that the Arachis genome has segmented synteny relationship to the other legumes. The comparative maps in legumes, integrated tetraploid consensus maps, and genome-specific diploid maps will increase the genetic and genomic understanding of Arachis and should facilitate molecular breeding.

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  • Single Nucleotide Polymorphism Analysis of a Trichoderma reesei Hyper-Cellulolytic Mutant Developed in Japan International journal

    Juliano de Oliveira Porciuncula, Takanori Furukawa, Kazuki Mori, Yosuke Shida, Hideki Hirakawa, Kosuke Tashiro, Satoru Kuhara, Satoshi Nakagawa, Yasushi Morikawa, Wataru Ogasawara

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY   77 ( 3 )   534 - 543   2013.3   ISSN:0916-8451 eISSN:1347-6947

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    The ascomycete Trichoderma reesei is known as one of the most prolific producers of plant biomass-degrading enzymes. While several mutant strains have been developed by mutagenesis to improve enzyme productivity for a variety of industrial applications, little is known about the mechanical basis of these improvements. A genomic sequence comparison of mutant and wild-type strains was undertaken to provide new in-sights in this regard. We identified a number of single-nucleotide polymorphisms (SNPs) after sequencing the genome of a hyper-cellulolytic T. reesei strain, PC-3-7, with a next-generation sequencer. Of these, the SNP detected in cre1, the carbon catabolite repressor gene, was found to be responsible for increased cellulase production. Further comparative genomic analysis enabled the identification of an SNP that correlated well with high cellulase production in a T. reesei mutant. These results provide a better understanding of the genetic changes induced by classical mutagenesis and bow they correlate with desirable phenotypes in filamentous fungi.

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  • Construction of an Integrated High Density Simple Sequence Repeat Linkage Map in Cultivated Strawberry (Fragaria x ananassa) and its Applicability International journal

    Sachiko N. Isobe, Hideki Hirakawa, Shusei Sato, Fumi Maeda, Masami Ishikawa, Toshiki Mori, Yuko Yamamoto, Kenta Shirasawa, Mitsuhiro Kimura, Masanobu Fukami, Fujio Hashizume, Tomoko Tsuji, Shigemi Sasamoto, Midori Kato, Keiko Nanri, Hisano Tsuruoka, Chiharu Minami, Chika Takahashi, Tsuyuko Wada, Akiko Ono, Kumiko Kawashima, Naomi Nakazaki, Yoshie Kishida, Mitsuyo Kohara, Shinobu Nakayama, Manabu Yamada, Tsunakazu Fujishiro, Akiko Watanabe, Satoshi Tabata

    DNA RESEARCH   20 ( 1 )   79 - 92   2013.2   ISSN:1340-2838 eISSN:1756-1663

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    The cultivated strawberry (Fragaria x ananassa) is an octoploid (2n = 8x = 56) of the Rosaceae family whose genomic architecture is still controversial. Several recent studies support the AAA'A'BBB'B' model, but its complexity has hindered genetic and genomic analysis of this important crop. To overcome this difficulty and to assist genome-wide analysis of F. x ananassa, we constructed an integrated linkage map by organizing a total of 4474 of simple sequence repeat (SSR) markers collected from published Fragaria sequences, including 3746 SSR markers [Fragaria vesca expressed sequence tag (EST)-derived SSR markers] derived from F. vesca ESTs, 603 markers (F. x ananassa EST-derived SSR markers) from F. x ananassa ESTs, and 125 markers (F. x ananassa transcriptome-derived SSR markers) from F. x ananassa transcripts. Along with the previously published SSR markers, these markers were mapped onto five parent-specific linkage maps derived from three mapping populations, which were then assembled into an integrated linkage map. The constructed map consists of 1856 loci in 28 linkage groups (LGs) that total 2364.1 cM in length. Macrosynteny at the chromosome level was observed between the LGs of F. x ananassa and the genome of F. vesca. Variety distinction on 129 F. x ananassa lines was demonstrated using 45 selected SSR markers.

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  • PhoB regulates the survival of Bacteroides fragilis in peritoneal abscesses. International journal

    Shin Wakimoto, Haruyuki Nakayama-Imaohji, Minoru Ichimura, Hidetoshi Morita, Hideki Hirakawa, Tetsuya Hayashi, Koji Yasutomo, Tomomi Kuwahara

    PloS one   8 ( 1 )   e53829   2013.1   ISSN:1932-6203

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    In response to phosphate limitation, bacteria employ the Pho regulon, a specific regulatory network for phosphate acquisition. The two-component signal transduction system of PhoRB plays a crucial role in the induction of Pho regulon genes, leading to the adaptation to phosphate starvation. Herein, we identified the PhoRB system in Bacteroides fragilis, a commensal gut bacterium, and evaluated its role in gut colonization and survival in peritoneal abscesses. BF1575 and BF1576 encoded PhoR (sensor histidine kinase) and PhoB (response regulator) in the sequenced B. fragilis strain YCH46, respectively. Transcriptome analysis revealed that deletion of phoB affected the expression of 585 genes (more than 4-fold change) in B. fragilis, which included genes for stress response (chaperons and heat shock proteins), virulence (capsular polysaccharide biosynthesis) and phosphate metabolism. Deletion of phoB reduced the ability of the bacterium to persist in peritoneal abscesses induced by an intra-abdominal challenge of B. fragilis. Furthermore, PhoB was necessary for survival of this anaerobe in peritoneal abscesses but not for in vitro growth in rich media or in intestinal colonization. These results indicate that PhoB plays an important role in the survival of B. fragilis under stressful extraintestinal conditions.

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  • Genome-wide SNP marker development and QTL identification for Genomic selection in red clover

    S. Isobe, B. Boller, I. Klimenko, S. Kölliker, J. C. Rana, T. R. Sharma, K. Shirasawa, H. Hirakawa, S. Sato, S. Tabata

    Breeding Strategies for Sustainable Forage and Turf Grass Improvement   29 - 36   2013.1

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    © Springer Science+Business Media Dordrecht 2013. Genomic selection (GS) has experienced remarkable advances in genome technologies over the past few years. However, employing GS for forage breeding has been considered difficult because forage species generally show short linkage disequilibrium (LD) across the genome. To elongate the LD, an Advanced Intercross Line (AIL) population was generated from crosses between six individuals originating from Switzerland, Russia and Japan. The suitability of this population was demonstrated for GS or association analysis. For high throughput genotyping, single nucleotide polymorphism (SNP) markers were developed by comparing transcriptome sequences obtained from two red clover individuals. An Illumina Golden Gate platform for 1,536 candidate SNPs was used for polymorphic analysis in the AIL population.A total of 784 SNP markers were identified as polymorphic. In addition, 75 polymorphic SSR markers were used for genotyping the AIL population. Approximately 200 plants each were established in 2010 in the fields of Palampur, Moscow region, Zurich and Chiba. Seed yields, flowering characteristics and morphological traits were evaluated in each region. Significant QTLs and QTL interactions were identified for the traits investigated by GMM analysis. The results suggest that the AIL population can be used for GS and association analysis.

    DOI: 10.1007/978-94-007-4555-1_3

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  • Commonalities and Differences among Symbiosis Islands of Three <i>Mesorhizobium loti</i> Strains

    Kasai-Maita Hiroko, Hirakawa Hideki, Nakamura Yasukazu, Kaneko Takakazu, Miki Kumiko, Maruya Jumpei, Okazaki Shin, Tabata Satoshi, Saeki Kazuhiko, Sato Shusei

    Microbes and Environments   28 ( 2 )   275 - 278   2013   ISSN:13426311 eISSN:13474405

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    To shed light on the breadth of the host range of <i>Mesorhizobium loti</i> strain NZP2037, we determined the sequence of the NZP2037 symbiosis island and compared it with those of strain MAFF303099 and R7A islands. The determined 533 kb sequence of NZP2037 symbiosis island, on which 504 genes were predicted, implied its integration into a phenylalanine-tRNA gene and subsequent genome rearrangement. Comparative analysis revealed that the core regions of the three symbiosis islands consisted of 165 genes. We also identified several NZP2037-specific genes with putative functions in nodulation-related events, suggesting that these genes contribute to broaden the host range of NZP2037.<br>

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  • DNA marker applications to molecular genetics and genomics in tomato

    Shirasawa Kenta, Hirakawa Hideki

    Breeding Science   63 ( 1 )   21 - 30   2013   ISSN:13447610 eISSN:13473735

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    Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of the earliest targets in plants. The developed DNA markers have been applied to the construction of genetic linkage maps and the resultant maps have contributed to quantitative trait locus (QTL) and gene mappings for agronomically important traits, as well as to comparative genomics of Solanaceae. The recently released whole genome sequences of tomato enable us to develop large numbers of DNA markers comparatively easily, and even promote new genotyping methods without DNA markers. In addition, databases for genomes, DNA markers, genetic linkage maps and other omics data, e.g., transcriptome, proteome, metabolome and phenome information, will provide useful information for molecular breeding in tomatoes. The use of DNA marker technologies in conjunction with new breeding techniques will promise to advance tomato breeding.

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    Other Link: https://jlc.jst.go.jp/DN/JALC/10017622287?from=CiNii

  • Spatiotemporal regulation of the ubiquitinated cargo-binding activity of Rabex-5 in the endocytic pathway. International journal

    Yoshikatsu Aikawa, Hideki Hirakawa, Sangho Lee

    The Journal of biological chemistry   287 ( 48 )   40586 - 40597   2012.11   eISSN:1083-351X

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    BACKGROUND: The regulatory mechanism underlying the interaction of the Rabex-5 MIU domain with ubiquitinated cargos remains unclear. RESULTS: Rabex-5 guanine nucleotide exchange factor (GEF) mutants affected interactions of ubiquitinated cargos. CONCLUSION: GDP/GTP exchange in the GEF domain controls the MIU domain interactions with the ubiquitinated cargos. SIGNIFICANCE: Rabex-5 GEF activity acts as an intramolecular switch for spatiotemporal trafficking of the ubiquitinated cargos. Ubiquitin (Ub)-dependent endocytosis of membrane proteins requires precise molecular recognition of ubiquitinated cargo by Ub-binding proteins (UBPs). Many UBPs are often themselves monoubiquitinated, a mechanism referred to as coupled monoubiquitination, which prevents them from binding in trans to the ubiquitinated cargo. However, the spatiotemporal regulatory mechanism underlying the interaction of UBPs with the ubiquitinated cargo, via their Ub-binding domains (UBDs) remains unclear. Previously, we reported the interaction of Rabex-5, a UBP and guanine nucleotide exchange factor (GEF) for Rab5, with ubiquitinated neural cell adhesion molecule L1, via its motif interacting with Ub (MIU) domain. This interaction is critical for the internalization and sorting of the ubiquitinated L1 into endosomal/lysosomal compartments. The present study demonstrated that the interaction of Rabex-5 with Rab5 depends specifically on interaction of the MIU domain with the ubiquitinated L1 to drive its internalization. Notably, impaired GEF mutants and the Rabex-5(E213A) mutant increased the flexibility of the hinge region in the HB-VPS9 tandem domain, which significantly affected their interactions with the ubiquitinated L1. In addition, GEF mutants increased the catalytic efficiency, which resulted in a reduced interaction with the ubiquitinated L1. Furthermore, the coupled monoubiquitination status of Rabex-5 was found to be significantly associated with interaction of Rabex-5 and the ubiquitinated L1. Collectively, our study reveals a novel mechanism, wherein the GEF activity of Rabex-5 acts as an intramolecular switch orchestrating ubiquitinated cargo-binding activity and coupled monoubiquitination to permit the spatiotemporal dynamic exchange of the ubiquitinated cargos.

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  • Complete genome sequence of Bacillus cereus NC7401, which produces high levels of the emetic toxin cereulide. International journal

    Akira Takeno, Akira Okamoto, Keizo Tori, Kenshiro Oshima, Hideki Hirakawa, Hidehiro Toh, Norio Agata, Keiko Yamada, Naotake Ogasawara, Tetsuya Hayashi, Tohru Shimizu, Satoru Kuhara, Masahira Hattori, Michio Ohta

    Journal of bacteriology   194 ( 17 )   4767 - 4768   2012.9   ISSN:0021-9193

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    We report the complete and annotated genome sequence of Bacillus cereus NC7401, a representative of the strain group that causes emetic-type food poisoning. The emetic toxin, cereulide, is produced by a nonribosomal protein synthesis (NRPS) system that is encoded by a gene cluster on a large resident plasmid, pNCcld.

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  • Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology. International journal

    Koji Tanase, Chikako Nishitani, Hideki Hirakawa, Sachiko Isobe, Satoshi Tabata, Akemi Ohmiya, Takashi Onozaki

    BMC genomics   13   292 - 292   2012.7   ISSN:1471-2164

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    BACKGROUND: Carnation (Dianthus caryophyllus L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST) database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology. RESULTS: We constructed a normalized cDNA library and a 3'-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an Arabidopsis sequence database, and 61.8% (23,380) of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO) and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs) in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway. CONCLUSIONS: We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.

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  • Complete genome sequence of Helicobacter cinaedi strain PAGU611, isolated in a case of human bacteremia. International journal

    Takatsugu Goto, Yoshitoshi Ogura, Hideki Hirakawa, Junko Tomida, Yuji Morita, Takaaki Akaike, Tetsuya Hayashi, Yoshiaki Kawamura

    Journal of bacteriology   194 ( 14 )   3744 - 3745   2012.7   ISSN:0021-9193

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    We report the complete genome sequence of Helicobacter cinaedi strain PAGU611, isolated in a case of human bacteremia. The PAGU611 genome comprises a 2,078,348-bp chromosome and a 23,054-bp plasmid. The chromosome contains a unique genomic island, encoding a type VI secretion system and clustered regularly interspaced short palindromic repeat (CRISPR) loci.

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  • In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut International journal

    Kenta Shirasawa, Padmalatha Koilkonda, Koh Aoki, Hideki Hirakawa, Satoshi Tabata, Manabu Watanabe, Makoto Hasegawa, Hiroyuki Kiyoshima, Shigeru Suzuki, Chikara Kuwata, Yoshiki Naito, Tsutomu Kuboyama, Akihiro Nakaya, Shigemi Sasamoto, Akiko Watanabe, Midori Kato, Kumiko Kawashima, Yoshie Kishida, Mitsuyo Kohara, Atsushi Kurabayashi, Chika Takahashi, Hisano Tsuruoka, Tsuyuko Wada, Sachiko Isobe

    BMC PLANT BIOLOGY   12   80 - 80   2012.6   ISSN:1471-2229

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    Background: Peanut (Arachis hypogaea) is an autogamous allotetraploid legume (2n = 4x = 40) that is widely cultivated as a food and oil crop. More than 6,000 DNA markers have been developed in Arachis spp., but high-density linkage maps useful for genetics, genomics, and breeding have not been constructed due to extremely low genetic diversity. Polymorphic marker loci are useful for the construction of such high-density linkage maps. The present study used in silico analysis to develop simple sequence repeat-based and transposon-based markers.Results: The use of in silico analysis increased the efficiency of polymorphic marker development by more than 3-fold. In total, 926 (34.2%) of 2,702 markers showed polymorphisms between parental lines of the mapping population. Linkage analysis of the 926 markers along with 253 polymorphic markers selected from 4,449 published markers generated 21 linkage groups covering 2,166.4 cM with 1,114 loci. Based on the map thus produced, 23 quantitative trait loci (QTLs) for 15 agronomical traits were detected. Another linkage map with 326 loci was also constructed and revealed a relationship between the genotypes of the FAD2 genes and the ratio of oleic/linoleic acid in peanut seed.Conclusions: In silico analysis of polymorphisms increased the efficiency of polymorphic marker development, and contributed to the construction of high-density linkage maps in cultivated peanut. The resultant maps were applicable to QTL analysis. Marker subsets and linkage maps developed in this study should be useful for genetics, genomics, and breeding in Arachis. The data are available at the Kazusa DNA Marker Database (http://marker.kazusa.or.jp).

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  • Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp. International journal

    Padmalatha Koilkonda, Shusei Sato, Satoshi Tabata, Kenta Shirasawa, Hideki Hirakawa, Hiroe Sakai, Shigemi Sasamoto, Akiko Watanabe, Tsuyuko Wada, Yoshie Kishida, Hisano Tsuruoka, Tsunakazu Fujishiro, Manabu Yamada, Mitsuyo Kohara, Shigeru Suzuki, Makoto Hasegawa, Hiroyuki Kiyoshima, Sachiko Isobe

    Molecular Breeding   30 ( 1 )   125 - 138   2012.6   ISSN:1380-3743 eISSN:1572-9788

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    Large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed in peanut (Arachis hypogaea L.) to obtain more informative genetic markers. A total of 10,102 potential non-redundant EST sequences, including 3,445 contigs and 6,657 singletons, were generated from cDNA libraries of the gynophore, roots, leaves and seedlings. A total of 3,187 primer pairs were designed on flanking regions of SSRs, some of which allowed one and two base mismatches. Among the 3,187 markers generated, 2,540 (80%) were trinucleotide repeats, 302 (9%) were dinucleotide repeats, and 345 (11%) were tetranucleotide repeats. Pre-polymorphic analyses of 24 Arachis accessions were performed using 10% polyacrylamide gels. A total of 1,571 EST-SSR markers showing clear polymorphisms were selected for further polymorphic analysis with a Fluoro-fragment Analyzer. The 16 Arachis accessions examined included cultivated peanut varieties as well as diploid species with the A or B genome. Altogether 1,281 (81. 5%) of the 1,571 markers were polymorphic among the 16 accessions, and 366 (23. 3%) were polymorphic among the 12 cultivated varieties. Diversity analysis was performed and the genotypes of all 16 Arachis accessions showed similarity coefficients ranging from 0. 37 to 0. 97. © 2011 The Author(s).

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  • The tomato genome sequence provides insights into fleshy fruit evolution

    Shusei Sato, Satoshi Tabata, Hideki Hirakawa, Erika Asamizu, Kenta Shirasawa, Sachiko Isobe, Takakazu Kaneko, Yasukazu Nakamura, Daisuke Shibata, Koh Aoki, Michael Egholm, James Knight, Robert Bogden, Changbao Li, Yang Shuang, Xun Xu, Shengkai Pan, Shifeng Cheng, Xin Liu, Yuanyuan Ren, Jun Wang, Alessandro Albiero, Francesca Dal Pero, Sara Todesco, Joyce Van Eck, Robert M. Buels, Aureliano Bombarely, Joseph R. Gosselin, Minyun Huang, Jonathan A. Leto, Naama Menda, Susan Strickler, Linyong Mao, Shan Gao, Isaak Y. Tecle, Thomas York, Yi Zheng, Julia T. Vrebalov, JeMin Lee, Silin Zhong, Lukas A. Mueller, Willem J. Stiekema, Paolo Ribeca, Tyler Alioto, Wencai Yang, Sanwen Huang, Yongchen Du, Zhonghua Zhang, Jianchang Gao, Yanmei Guo, Xiaoxuan Wang, Ying Li, Jun He, Chuanyou Li, Zhukuan Cheng, Jianru Zuo, Jianfeng Ren, Jiuhai Zhao, Liuhua Yan, Hongling Jiang, Bao Wang, Hongshuang Li, Zhenjun Li, Fuyou Fu, Bingtang Chen, Bin Han, Qi Feng, Danlin Fan, Ying Wang, Hongqing Ling, Yongbiao Xue, Doreen Ware, W. Richard McCombie, Zachary B. Lippman, Jer-Ming Chia, Ke Jiang, Shiran Pasternak, Laura Gelley, Melissa Kramer, Lorinda K. Anderson, Song-Bin Chang, Suzanne M. Royer, Lindsay A. Shearer, Stephen M. Stack, Jocelyn K. C. Rose, Yimin Xu, Nancy Eannetta, Antonio J. Matas, Ryan McQuinn, Steven D. Tanksley, Francisco Camara, Roderic Guigo, Stephane Rombauts, Jeffrey Fawcett, Yves Van de Peer, Dani Zamir, Chunbo Liang, Manuel Spannagl, Heidrun Gundlach, Remy Bruggmann, Klaus Mayer, Zhiqi Jia, Junhong Zhang, Zhibiao Ye, Gerard J. Bishop, Sarah Butcher, Rosa Lopez-Cobollo, Daniel Buchan, Ioannis Filippis, James Abbott, Rekha Dixit, Manju Singh, Archana Singh, Jitendra Kumar Pal, Awadhesh Pandit, Pradeep Kumar Singh, Ajay Kumar Mahato, Vivek Dogra, Kishor Gaikwad, Tilak Raj Sharma, Trilochan Mohapatra, Nagendra Kumar Singh, Mathilde Causse, Christophe Rothan, Thomas Schiex, Celine Noirot, Arnaud Bellec, Christophe Klopp, Corinne Delalande, Helene Berges, Jerome Mariette, Pierre Frasse, Sonia Vautrin, Mohamed Zouine, Alain Latche, Christine Rousseau, Farid Regad, Jean-Claude Pech, Murielle Philippot, Mondher Bouzayen, Pierre Pericard, Sonia Osorio, Asuncion Fernandez del Carmen, Antonio Monforte, Antonio Granell, Rafael Fernandez-Munoz, Mariana Conte, Gabriel Lichtenstein, Fernando Carrari, Gianluca De Bellis, Fabio Fuligni, Clelia Peano, Silvana Grandillo, Pasquale Termolino, Marco Pietrella, Elio Fantini, Giulia Falcone, Alessia Fiore, Giovanni Giuliano, Loredana Lopez, Paolo Facella, Gaetano Perrotta, Loretta Daddiego, Glenn Bryan, Modesto Orozco, Xavier Pastor, David Torrents, Keygene N. V. Marco G. M. van Schriek, Richard M. C. Feron, Jan van Oeveren, Peter de Heer, Lorena daPonte, Saskia Jacobs-Oomen, Mike Cariaso, Marcel Prins, Michiel J. T. van Eijk, Antoine Janssen, Mark J. J. van Haaren, Sung-Hwan Jo, Jungeun Kim, Suk-Yoon Kwon, Sangmi Kim, Dal-Hoe Koo, Sanghyeob Lee, Cheol-Goo Hur, Christopher Clouser, Alain Rico, Asis Hallab, Christiane Gebhardt, Kathrin Klee, Anika Joecker, Jens Warfsmann, Ulrike Goebel, Shingo Kawamura, Kentaro Yano, Jamie D. Sherman, Hiroyuki Fukuoka, Satomi Negoro, Sarita Bhutty, Parul Chowdhury, Debasis Chattopadhyay, Erwin Datema, Sandra Smit, Eliog. W. M. Schijlen, Jose van de Belt, Jan C. van Haarst, Sander A. Peters, Marjo J. van Staveren, Marleen H. C. Henkens, Paul J. W. Mooyman, Thamara Hesselink, Roeland C. H. J. van Ham, Guoyong Jiang, Marcus Droege, Doil Choi, Byung-Cheol Kang, Byung Dong Kim, Minkyu Park, Seungill Kim, Seon-In Yeom, Yong-Hwan Lee, Yang-Do Choi, Guangcun Li, Jianwei Gao, Yongsheng Liu, Shengxiong Huang, Victoria Fernandez-Pedrosa, Carmen Collado, Sheila Zuniga, Guoping Wang, Rebecca Cade, Robert A. Dietrich, Jane Rogers, Sandra Knapp, Zhangjun Fei, Ruth A. White, Theodore W. Thannhauser, James J. Giovannoni, Miguel Angel Botella, Louise Gilbert, Ramon Gonzalez, Jose Luis Goicoechea, Yeisoo Yu, David Kudrna, Kristi Collura, Marina Wissotski, Rod Wing, Heiko Schoof, Blake C. Meyers, Aishwarya Bala Gurazada, Pamela J. Green, Saloni Mathur, Shailendra Vyas, Amolkumar U. Solanke, Rahul Kumar, Vikrant Gupta, Arun K. Sharma, Paramjit Khurana, Jitendra P. Khurana, Akhilesh K. Tyagi, Tamas Dalmay, Irina Mohorianu, Brandon Walts, Srikar Chamala, W. Brad Barbazuk, Jingping Li, Hui Guo, Tae-Ho Lee, Yupeng Wang, Dong Zhang, Andrew H. Paterson, Xiyin Wang, Haibao Tang, Amalia Barone, Maria Luisa Chiusano, Maria Raffaella Ercolano, Nunzio D'Agostino, Miriam Di Filippo, Alessandra Traini, Walter Sanseverino, Luigi Frusciante, Graham B. Seymour, Mounir Elharam, Ying Fu, Axin Hua, Steven Kenton, Jennifer Lewis, Shaoping Lin, Fares Najar, Hongshing Lai, Baifang Qin, Chunmei Qu, Ruihua Shi, Douglas White, James White, Yanbo Xing, Keqin Yang, Jing Yi, Ziyun Yao, Liping Zhou, Bruce A. Roe, Alessandro Vezzi, Michela D'Angelo, Rosanna Zimbello, Riccardo Schiavon, Elisa Caniato, Chiara Rigobello, Davide Campagna, Nicola Vitulo, Giorgio Valle, David R. Nelson, Emanuele De Paoli, Dora Szinay, Hans H. de Jong, Yuling Bai, Richard G. F. Visser, Rene M. Klein Lankhorst, Helen Beasley, Karen McLaren, Christine Nicholson, Claire Riddle, Giulio Gianese

    NATURE   485 ( 7400 )   635 - 641   2012.5   ISSN:0028-0836 eISSN:1476-4687

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    Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

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  • Comparative Genetic Mapping and Discovery of Linkage Disequilibrium Across Linkage Groups in White Clover (Trifolium repens L.) International journal

    Sachiko N. Isobe, Hiroshi Hisano, Shusei Sato, Hideki Hirakawa, Kenji Okumura, Kenta Shirasawa, Shigemi Sasamoto, Akiko Watanabe, Tsuyuko Wada, Yoshie Kishida, Hisano Tsuruoka, Tsunakazu Fujishiro, Manabu Yamada, Mistuyo Kohara, Satoshi Tabata

    G3-GENES GENOMES GENETICS   2 ( 5 )   607 - 617   2012.5   ISSN:2160-1836

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    White clover (Trifolium repens L.) is an allotetraploid species (2n - 4X - 32) that is widely distributed in temperate regions and cultivated as a forage legume. In this study, we developed expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers, constructed linkage maps, and performed comparative mapping with other legume species. A total of 7982 ESTs that could be assembled into 5400 contigs and 2582 singletons were generated. Using the EST sequences that were obtained, 1973 primer pairs to amplify EST-derived SSR markers were designed and used for linkage analysis of 188 F-1 progenies, which were generated by a cross between two Japanese plants, '273-7' and 'T17-349,' with previously published SSR markers. An integrated linkage map was constructed by combining parental-specific maps, which consisted of 1743 SSR loci on 16 homeologous linkage groups with a total length of 2511 cM. The primer sequences of the developed EST-SSR markers and their map positions are available on http://clovergarden.jp/. Linkage disequilibrium (LD) was observed on 9 of 16 linkage groups of a parental-specific map. The genome structures were compared among white clover, red clover (T. pratense L.), Medicago truncatula, and Lotus japonicus. Macrosynteny was observed across the four legume species. Surprisingly, the comparative genome structure between white clover and M. truncatula had a higher degree of conservation than that of the two clover species.

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  • Characterization of active miniature inverted-repeat transposable elements in the peanut genome International journal

    Kenta Shirasawa, Hideki Hirakawa, Satoshi Tabata, Makoto Hasegawa, Hiroyuki Kiyoshima, Sigeru Suzuki, Sigemi Sasamoto, Akiko Watanabe, Tsunakazu Fujishiro, Sachiko Isobe

    THEORETICAL AND APPLIED GENETICS   124 ( 8 )   1429 - 1438   2012.5   ISSN:0040-5752 eISSN:1432-2242

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    Miniature inverted-repeat transposable elements (MITEs), some of which are known as active non-autonomous DNA transposons, are found in the genomes of plants and animals. In peanut (Arachis hypogaea), AhMITE1 has been identified in a gene for fatty-acid desaturase, and possessed excision activity. However, the AhMITE1 distribution and frequency of excision have not been determined for the peanut genome. In order to characterize AhMITE1s, their genomic diversity and transposition ability was investigated. Southern blot analysis indicated high AhMITE1 copy number in the genomes of A. hypogaea, A. magna and A. monticola, but not in A. duranensis. A total of 504 AhMITE1s were identified from the MITE-enriched genomic libraries of A. hypogaea. The representative AhMITE1s exhibited a mean length of 205.5 bp and a GC content of 30.1%, with AT-rich, 9 bp target site duplications and 25 bp terminal inverted repeats. PCR analyses were performed using primer pairs designed against both flanking sequences of each AhMITE1. These analyses detected polymorphisms at 169 out of 411 insertional loci in the four peanut lines. In subsequent analyses of 60 gamma-irradiated mutant lines, four AhMITE1 excisions showed footprint mutations at the 109 loci tested. This study characterizes AhMITE1s in peanut and discusses their use as DNA markers and mutagens for the genetics, genomics and breeding of peanut and its relatives.

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  • Establishment of a Lotus japonicus gene tagging population using the exon-targeting endogenous retrotransposon LORE1 International journal

    Eigo Fukai, Takashi Soyano, Yosuke Umehara, Shinobu Nakayama, Hideki Hirakawa, Satoshi Tabata, Shusei Sato, Makoto Hayashi

    PLANT JOURNAL   69 ( 4 )   720 - 730   2012.2   ISSN:0960-7412

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    We established a gene tagging population of the model legume Lotus japonicus using an endogenous long terminal repeat (LTR) retrotransposon Lotus Retrotransposon 1 (LORE1). The population was composed of 2450 plant lines, from which a total of 4532 flanking sequence tags of LORE1 were recovered by pyrosequencing. The two-dimensional arrangement of the plant population, together with the use of multiple identifier sequences in the primers used to amplify the flanking regions, made it possible to trace insertions back to the original plant lines. The large-scale detection of new LORE1 insertion sites revealed a preference for genic regions, especially in exons of protein-coding genes, which is an interesting feature to consider in the interaction between host genomes and chromoviruses, to which LORE1 belongs, a class of retrotransposon widely distributed among plants. Forward screening of the symbiotic mutants from the population succeeded to identify five symbiotic mutants of known genes. These data suggest that LORE1 is robust as a genetic tool.

    DOI: 10.1111/j.1365-313X.2011.04826.x

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  • Genome-wide phylogenetic analysis of differences in thermotolerance among closely related Acetobacter pasteurianus strains International journal

    Minenosuke Matsutani, Hideki Hirakawa, Natsaran Saichana, Wichai Soemphol, Toshiharu Yakushi, Kazunobu Matsushita

    MICROBIOLOGY-SGM   158 ( Pt 1 )   229 - 239   2012.1   ISSN:1350-0872 eISSN:1465-2080

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    Acetobacter pasteurianus is a Gram-negative strictly aerobic bacterium that is widely used for the industrial production of vinegar. Three Acetobacter pasteurianus strains, SKU1108, NBRC 3283 and IFO 3191, have the same 16S rRNA sequence (100% sequence identity) but show differences in thermotolerance. To clarify the relationships between phylogeny and thermotolerance of these strains, genome-wide analysis of these three strains was performed. Concatenated phylogenetic analysis of a dataset of 1864 orthologues has shown that the more thermotolerant strains, SKU1108 and NBRC 3283, are more closely related to each other than to the more thermosensitive strain, IFO 3191. In addition, we defined a dataset of 2010 unique orthologues among these three strains, and compared the frequency of amino acid mutations among them. Genes involved in translation, transcription and signal transduction are highly conserved among each unique orthologous dataset. The results also showed that there are several genes with increased mutation rates in IFO 3191 compared with the thermotolerant strains, SKU1108 and NBRC 3283. Analysis of the mutational directions of these genes suggested that some of them might be correlated with the thermosensitivity of IFO 3191. Concatenated phylogenetic analysis of these closely related strains revealed that there is a phylogenetic relationship associated with this phenotype among the thermotolerant and thermosensitive strains.

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  • Complete Genome Sequence of <i>Bradyrhizobium</i> sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs

    Okubo Takashi, Tsukui Takahiro, Maita Hiroko, Okamoto Shinobu, Oshima Kenshiro, Fujisawa Takatomo, Saito Akihiro, Futamata Hiroyuki, Hattori Reiko, Shimomura Yumi, Haruta Shin, Morimoto Sho, Wang Yong, Sakai Yoriko, Hattori Masahira, Aizawa Shin-ichi, Nagashima Kenji V. P., Masuda Sachiko, Hattori Tsutomu, Yamashita Akifumi, Bao Zhihua, Hayatsu Masahito, Kajiya-Kanegae Hiromi, Yoshinaga Ikuo, Sakamoto Kazunori, Toyota Koki, Nakao Mitsuteru, Kohara Mitsuyo, Anda Mizue, Niwa Rieko, Jung-Hwan Park, Sameshima-Saito Reiko, Tokuda Shin-ichi, Yamamoto Sumiko, Yamamoto Syuji, Yokoyama Tadashi, Akutsu Tomoko, Nakamura Yasukazu, Nakahira-Yanaka Yuka, Takada Hoshino Yuko, Hirakawa Hideki, Mitsui Hisayuki, Terasawa Kimihiro, Itakura Manabu, Sato Shusei, Ikeda-Ohtsubo Wakako, Sakakura Natsuko, Kaminuma Eli, Minamisawa Kiwamu

    Microbes and Environments   27 ( 3 )   306 - 315   2012   ISSN:13426311 eISSN:13474405

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    <i>Bradyrhizobium</i> sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to <i>Bradyrhizobium japonicum</i> USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (<i>groELS3</i>) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a <i>nif</i> (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.<br>

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    Other Link: http://orcid.org/0000-0002-3705-2459

  • Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms. Reviewed International journal

    Erika Asamizu, Kenta Shirasawa, Hideki Hirakawa, Shusei Sato, Satoshi Tabata, Kentaro Yano, Tohru Ariizumi, Daisuke Shibata, Hiroshi Ezura

    International journal of plant genomics   2012   437026 - 437026   2012   ISSN:1687-5370

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    A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, "Heinz 1706." By referring to the "Heinz 1706" physical map and by eliminating redundant or nonsignificant hits, 28,804 "unique pair ends" and 8,263 "unique ends" were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database.

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  • Upgraded genomic information of <i>Jatropha curcas</i> L.

    Hirakawa Hideki, Tsuchimoto Suguru, Sakai Hiroe, Nakayama Shinobu, Fujishiro Tsunakazu, Kishida Yoshie, Kohara Mitsuyo, Watanabe Akiko, Yamada Manabu, Aizu Tomoyuki, Toyoda Atsushi, Fujiyama Asao, Tabata Satoshi, Fukui Kiichi, Sato Shusei

    Plant Biotechnology   29 ( 2 )   123 - 130   2012   ISSN:13424580 eISSN:13476114

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    In order to upgrade the genome sequence information of <i>J. curcas</i> L., we integrated <i>de novo</i> assembly of a total of 537 million paired-end reads generated from the Illumina sequencing platform into the current genome assembly which was obtained by a combination of the conventional Sanger method and the Roche/454 sequencing platform. The total length of the upgraded genome sequences thus obtained was 297,661,187 bp consisting of 39,277 contigs. The average and N50 lengths of the generated contigs were 7,579 bp and 15,950 bp, both of which were increased fourfold from the previous genome assembly. Along with genome sequence upgrading, the currently available transcriptome data were collected from the public databases and assembled into 19,454 tentative consensus sequences. Based on a comparison between these tentative consensus sequences of transcripts and the predictions of computer programs, a total of 30,203 complete and partial structures of protein-encoding genes were deduced. The number of genes with complete structures was increased about threefold from the previous genome annotation. By applying the upgraded genome sequence and predicted protein-coding gene information, the number and features of the tandemly arrayed genes, syntenic relations between Jatropha and other plant genomes, and structural features of transposable elements were investigated. The detailed information on the updated <i>J. curcas</i> genome is available at http://www.kazusa.or.jp/jatropha/.

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  • Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6(T) International journal

    Takakazu Kaneko, Hiroko Maita, Hideki Hirakawa, Nobukazu Uchiike, Kiwamu Minamisawa, Akiko Watanabe, Shusei Sato

    GENES   2 ( 4 )   763 - 787   2011.12   ISSN:2073-4425 eISSN:2073-4425

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    The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6(T) was determined. The genome of USDA6(T) is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6(T) and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.

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  • The genome of the mesopolyploid crop species Brassica rapa International journal

    Xiaowu Wang, Hanzhong Wang, Jun Wang, Rifei Sun, Jian Wu, Shengyi Liu, Yinqi Bai, Jeong-Hwan Mun, Ian Bancroft, Feng Cheng, Sanwen Huang, Xixiang Li, Wei Hua, Junyi Wang, Xiyin Wang, Michael Freeling, J. Chris Pires, Andrew H. Paterson, Boulos Chalhoub, Bo Wang, Alice Hayward, Andrew G. Sharpe, Beom-Seok Park, Bernd Weisshaar, Binghang Liu, Bo Li, Bo Liu, Chaobo Tong, Chi Song, Christopher Duran, Chunfang Peng, Chunyu Geng, Chushin Koh, Chuyu Lin, David Edwards, Desheng Mu, Di Shen, Eleni Soumpourou, Fei Li, Fiona Fraser, Gavin Conant, Gilles Lassalle, Graham J. King, Guusje Bonnema, Haibao Tang, Haiping Wang, Harry Belcram, Heling Zhou, Hideki Hirakawa, Hiroshi Abe, Hui Guo, Hui Wang, Huizhe Jin, Isobel A. P. Parkin, Jacqueline Batley, Jeong-Sun Kim, Jeremy Just, Jianwen Li, Jiaohui Xu, Jie Deng, Jin A. Kim, Jingping Li, Jingyin Yu, Jinling Meng, Jinpeng Wang, Jiumeng Min, Julie Poulain, Jun Wang, Katsunori Hatakeyama, Kui Wu, Li Wang, Lu Fang, Martin Trick, Matthew G. Links, Meixia Zhao, Mina Jin, Nirala Ramchiary, Nizar Drou, Paul J. Berkman, Qingle Cai, Quanfei Huang, Ruiqiang Li, Satoshi Tabata, Shifeng Cheng, Shu Zhang, Shujiang Zhang, Shunmou Huang, Shusei Sato, Silong Sun, Soo-Jin Kwon, Su-Ryun Choi, Tae-Ho Lee, Wei Fan, Xiang Zhao, Xu Tan, Xun Xu, Yan Wang, Yang Qiu, Ye Yin, Yingrui Li, Yongchen Du, Yongcui Liao, Yongpyo Lim, Yoshihiro Narusaka, Yupeng Wang, Zhenyi Wang, Zhenyu Li, Zhiwen Wang, Zhiyong Xiong, Zhonghua Zhang

    NATURE GENETICS   43 ( 10 )   1035 - U157   2011.10   ISSN:1061-4036 eISSN:1546-1718

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    We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

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  • An EST-SSR Linkage Map of Raphanus sativus and Comparative Genomics of the Brassicaceae International journal

    Kenta Shirasawa, Maki Oyama, Hideki Hirakawa, Shusei Sato, Satoshi Tabata, Takashi Fujioka, Chiaki Kimizuka-Takagi, Shigemi Sasamoto, Akiko Watanabe, Midori Kato, Yoshie Kishida, Mitsuyo Kohara, Chika Takahashi, Hisano Tsuruoka, Tsuyuko Wada, Takako Sakai, Sachiko Isobe

    DNA RESEARCH   18 ( 4 )   221 - 232   2011.8   ISSN:1340-2838 eISSN:1756-1663

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    Raphanus sativus (2n = 2x = 18) is a widely cultivated member of the family Brassicaceae, for which genomic resources are available only to a limited extent in comparison to many other members of the family. To promote more genetic and genomic studies and to enhance breeding programmes of R. sativus, we have prepared genetic resources such as complementary DNA libraries, expressed sequences tags (ESTs), simple sequence repeat (SSR) markers and a genetic linkage map. A total of 26 606 ESTs have been collected from seedlings, roots, leaves, and flowers, and clustered into 10 381 unigenes. Similarities were observed between the expression patterns of transcripts from R. sativus and those from representative members of the genera Arabidopsis and Brassica, indicating their functional relatedness. The EST sequence data were used to design 3800 SSR markers and consequently 630 polymorphic SSR loci and 213 reported marker loci have been mapped onto nine linkage groups, covering 1129.2 cM with an average distance of 1.3 cM between loci. Comparison of the mapped EST-SSR marker positions in R. sativus with the genome sequence of A. thaliana indicated that the Brassicaceae members have evolved from a common ancestor. It appears that genomic fragments corresponding to those of A. thaliana have been doubled and tripled in R. sativus. The genetic map developed here is expected to provide a standard map for the genetics, genomics, and molecular breeding of R. sativus as well as of related species. The resources are available at http://marker.kazusa.or.jp/Daikon.

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  • The lifestyle of the segmented filamentous bacterium: a non-culturable gut-associated immunostimulating microbe inferred by whole-genome sequencing. International journal

    Tomomi Kuwahara, Yositoshi Ogura, Kenshiro Oshima, Ken Kurokawa, Tadasuke Ooka, Hideki Hirakawa, Takehiko Itoh, Haruyuki Nakayama-Imaohji, Minoru Ichimura, Kikuji Itoh, Chieko Ishifune, Yoichi Maekawa, Koji Yasutomo, Masahira Hattori, Tetsuya Hayashi

    DNA research : an international journal for rapid publication of reports on genes and genomes   18 ( 4 )   291 - 303   2011.8   ISSN:1340-2838 eISSN:1756-1663

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    Numerous microbes inhabit the mammalian intestinal track and strongly impact host physiology; however, our understanding of this ecosystem remains limited owing to the high complexity of the microbial community and the presence of numerous non-culturable microbes. Segmented filamentous bacteria (SFBs), which are clostridia-related Gram-positive bacteria, are among such non-culturable populations and are well known for their unique morphology and tight attachment to intestinal epithelial cells. Recent studies have revealed that SFBs play crucial roles in the post-natal maturation of gut immune function, especially the induction of Th17 lymphocytes. Here, we report the complete genome sequence of mouse SFBs. The genome, which comprises a single circular chromosome of 1 620 005 bp, lacks genes for the biosynthesis of almost all amino acids, vitamins/cofactors and nucleotides, but contains a full set of genes for sporulation/germination and, unexpectedly, for chemotaxis/flagella-based motility. These findings suggest a triphasic lifestyle of the SFB, which comprises two types of vegetative (swimming and epicellular parasitic) phases and a dormant (spore) phase. Furthermore, SFBs encode four types of flagellin, three of which are recognized by Toll-like receptor 5 and could elicit the innate immune response. Our results reveal the non-culturability, lifestyle and immunostimulation mechanisms of SFBs and provide a genetic basis for the future development of the SFB cultivation and gene-manipulation techniques.

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  • Increased number of Arginine-based salt bridges contributes to the thermotolerance of thermotolerant acetic acid bacteria, Acetobacter tropicalis SKU1100 Reviewed International journal

    Minenosuke Matsutani, Hideki Hirakawa, Mitsuteru Nishikura, Wichai Soemphol, Ibnaof Ali Ibnaof Ali, Toshiharu Yakushi, Kazunobu Matsushita

    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   409 ( 1 )   120 - 124   2011.5   ISSN:0006-291X eISSN:1090-2104

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    Thermotolerant acetic acid bacteria (AAB), Acetobacter tropicalis SKU1100, can grow above 40 degrees C. To investigate the basis of its thermotolerance, we compared the genome of A. tropicalis SKU1100 with that of mesophilic AAB strain Acetobacter pasteurianus IFO3283-01. The comparative genomic study showed that amino acid substitutions from large to small residue and Lys to Arg occur in many orthologous genes. Furthermore, comparative modeling study was carried out with the orthologous proteins between SKU1100 and IFO3283-01 strains, indicating that the number of Arg-based salt bridges increased in protein models. Since it has been reported that Arg-based salt bridges are important factor for thermo-stability of protein structure, our results strongly suggest that the increased number of Arg-based salt bridges may contributes to the thermotolerance of A. tropicalis SKU1100 (the thermo-stability of proteins in A. tropicalis SKU1100). (C) 2011 Elsevier Inc. All rights reserved.

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  • [Time serial changes in the concentrations of the related agents to fetal Yusho--dioxin-like PCBs and PCBs].

    Nagayama J, Todaka T, Hirakawa H, Hori T, Kajiwara J, Yoshimura T

    Fukuoka igaku zasshi = Hukuoka acta medica   102 ( 4 )   116 - 22   2011.4   ISSN:0016-254X

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  • Classification of bacteria based on the biases of terminal amino acid residues. International journal

    Michio Asada, Hideki Hirakawa, Satoru Kuhara

    The protein journal   30 ( 4 )   290 - 297   2011.4   ISSN:1572-3887

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    The frequencies of amino acid residues are known to be biased at both terminal regions of amino acid sequences deduced from bacterial genomic DNA. To investigate whether or not the features of biases of amino acid residues at the terminal regions are related to the bacterial phylogeny, we calculated the normalized amino acid compositions at both terminal regions, and used these compositions to classify 144 bacteria by hierarchical clustering analysis. Our results showed that most of these bacteria were classified into taxonomic classes by the hierarchical clustering analysis that was based on the normalized amino acid compositions at the N-terminal region. Therefore, we concluded that the features of biases of the N-terminal amino acid residues were related to the bacterial phylogeny.

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  • Genome-wide phylogenetic analysis of Gluconobacter, Acetobacter, and Gluconacetobacter International journal

    Minenosuke Matsutani, Hideki Hirakawa, Toshiharu Yakushi, Kazunobu Matsushita

    FEMS MICROBIOLOGY LETTERS   315 ( 2 )   122 - 128   2011.2   ISSN:0378-1097 eISSN:1574-6968

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    Phylogenetic relationships among three genera, Gluconobacter, Acetobacter, and Gluconacetobacter, of acetic acid bacteria (AAB) are still unclear, although phylogenetic analysis using 16S rRNA gene sequence has shown that Gluconacetobacter diverged first from the ancestor of these three genera. Therefore, the relationships among these three genera were investigated by genome-wide phylogenetic analysis of AAB. Contrary to the results of 16S rRNA gene analysis, phylogenetic analysis of 293 enzymes involved in metabolism clearly showed that Gluconobacter separated first from its common ancestor with Acetobacter and Gluconacetobacter. In addition, we defined 753 unique orthologous proteins among five known complete genomes of AAB, and phylogenetic analysis was carried out using concatenated gene sequences of these 753 proteins. The result also showed that Gluconobacter separated first from its common ancestor with Acetobacter and Gluconacetobacter. Our results strongly suggest that Gluconobacter was the first to diverge from the common ancestor of Gluconobacter, Acetobacter, and Gluconacetobacter, a relationship that is in good agreement with the physiologies and habitats of these genera.

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  • Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. International journal

    Shusei Sato, Hideki Hirakawa, Sachiko Isobe, Eigo Fukai, Akiko Watanabe, Midori Kato, Kumiko Kawashima, Chiharu Minami, Akiko Muraki, Naomi Nakazaki, Chika Takahashi, Shinobu Nakayama, Yoshie Kishida, Mitsuyo Kohara, Manabu Yamada, Hisano Tsuruoka, Shigemi Sasamoto, Satoshi Tabata, Tomoyuki Aizu, Atsushi Toyoda, Tadasu Shin-i, Yohei Minakuchi, Yuji Kohara, Asao Fujiyama, Suguru Tsuchimoto, Shin'ichiro Kajiyama, Eri Makigano, Nobuko Ohmido, Nakako Shibagaki, Joyce A Cartagena, Naoki Wada, Tsutomu Kohinata, Alipour Atefeh, Shota Yuasa, Sachihiro Matsunaga, Kiichi Fukui

    DNA research : an international journal for rapid publication of reports on genes and genomes   18 ( 1 )   65 - 76   2011.2   ISSN:1340-2838 eISSN:1756-1663

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    The whole genome of Jatropha curcas was sequenced, using a combination of the conventional Sanger method and new-generation multiplex sequencing methods. Total length of the non-redundant sequences thus obtained was 285 858 490 bp consisting of 120 586 contigs and 29 831 singlets. They accounted for ~95% of the gene-containing regions with the average G + C content was 34.3%. A total of 40 929 complete and partial structures of protein encoding genes have been deduced. Comparison with genes of other plant species indicated that 1529 (4%) of the putative protein-encoding genes are specific to the Euphorbiaceae family. A high degree of microsynteny was observed with the genome of castor bean and, to a lesser extent, with those of soybean and Arabidopsis thaliana. In parallel with genome sequencing, cDNAs derived from leaf and callus tissues were subjected to pyrosequencing, and a total of 21 225 unigene data have been generated. Polymorphism analysis using microsatellite markers developed from the genomic sequence data obtained was performed with 12 J. curcas lines collected from various parts of the world to estimate their genetic diversity. The genomic sequence and accompanying information presented here are expected to serve as valuable resources for the acceleration of fundamental and applied research with J. curcas, especially in the fields of environment-related research such as biofuel production. Further information on the genomic sequences and DNA markers is available at http://www.kazusa.or.jp/jatropha/.

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  • Survey of the genetic information carried in the genome of Eucalyptus camaldulensis

    Hirakawa Hideki, Nakamura Yasukazu, Kaneko Takakazu, Isobe Sachiko, Sakai Hiroe, Kato Tomohiko, Hibino Takashi, Sasamoto Shigemi, Watanabe Akiko, Yamada Manabu, Nakayama Shinobu, Fujishiro Tsunakazu, Kishida Yoshie, Kohara Mitsuyo, Tabata Satoshi, Sato Shusei

    Plant Biotechnology   28 ( 5 )   471 - 480   2011   ISSN:13424580 eISSN:13476114

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    The genetic information in the genome of <i>Eucalyptus camaldulensis</i> was investigated by sequencing the genome and the cDNA using a combination of the conventional Sanger method and next-generation sequencing methods, followed by intensive bioinformatics analyses. The total length of the non-redundant genomic sequences thus obtained was 654,922,307 bp consisting of 81,246 scaffolds and 121,194 singlets. These sequences accounted for approximately 92% of the gene-containing regions with an average G+C content of 33.6%. A total of 77,121 complete and partial structures of protein-encoding genes have been deduced. Comparison of the genes mapped on the KEGG pathways or located in the KOG classification with those in other plant species revealed the characteristics of the <i>E. camaldulensis</i> genome, and it was found that 23 pathways contained enzymes present only in the <i>E. camaldulensis</i> genome. Polymorphism analysis using microsatellite markers developed from the genomic sequence data obtained was performed with six <i>Eucalyptus</i> species collected from various parts of the world to estimate their genetic diversity, and the usefulness of these markers was demonstrated. The genomic sequence and accompanying information presented here are expected to serve as valuable resources for the acceleration of fundamental and applied research with <i>Eucalyptus</i>, especially in the fields of paper production and industrial materials. Further information on the genomic and cDNA sequences and microsatellite markers is available at http://www.kazusa.or.jp/eucaly/.

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  • SNP Discovery and Linkage Map Construction in Cultivated Tomato International journal

    Kenta Shirasawa, Sachiko Isobe, Hideki Hirakawa, Erika Asamizu, Hiroyuki Fukuoka, Daniel Just, Christophe Rothan, Shigemi Sasamoto, Tsunakazu Fujishiro, Yoshie Kishida, Mitsuyo Kohara, Hisano Tsuruoka, Tsuyuko Wada, Yasukazu Nakamura, Shusei Sato, Satoshi Tabata

    DNA RESEARCH   17 ( 6 )   381 - 391   2010.12   ISSN:1340-2838

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    Few intraspecific genetic linkage maps have been reported for cultivated tomato, mainly because genetic diversity within Solanum lycopersicum is much less than that between tomato species. Single nucleotide polymorphisms (SNPs), the most abundant source of genomic variation, are the most promising source of polymorphisms for the construction of linkage maps for closely related intraspecific lines. In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato. Out of the 5607 SNP positions detected through in silico analysis, 1536 were selected for high-throughput genotyping of two mapping populations derived from crosses between 'Micro-Tom' and either 'Ailsa Craig' or 'M82'. A total of 1137 markers, including 793 out of the 1338 successfully genotyped SNPs, along with 344 simple sequence repeat and intronic polymorphism markers, were mapped onto two linkage maps, which covered 1467.8 and 1422.7 cM, respectively. The SNP markers developed were then screened against cultivated tomato lines in order to estimate the transferability of these SNPs to other breeding materials. The molecular markers and linkage maps represent a milestone in the genomics and genetics, and are the first step toward molecular breeding of cultivated tomato. Information on the DNA markers, linkage maps, and SNP genotypes for these tomato lines is available at http://www.kazusa.or.jp/tomato/.

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  • Identification of a two-component VirR/VirS regulon in Clostridium perfringens. International journal

    Kaori Ohtani, Hideki Hirakawa, Kousuke Tashiro, Satoko Yoshizawa, Satoru Kuhara, Tohru Shimizu

    Anaerobe   16 ( 3 )   258 - 264   2010.6   ISSN:1075-9964 eISSN:1095-8274

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    Clostridium perfringens, a Gram-positive anaerobic pathogen, is a causative agent of human gas gangrene that leads to severe rapid tissue destruction and can cause death within hours unless treated immediately. Production of several toxins is known to be controlled by the two-component VirR/VirS system involving a regulatory RNA (VR-RNA) in C. perfringens. To elucidate the precise regulatory network governed by VirR/VirS and VR-RNA, a series of microarray screening using VirR/VirS and VR-RNA-deficient mutants was performed. Finally, by qRT-PCR analysis, 147 genes (30 single genes and 21 putative operons) were confirmed to be under the control of the VirR/VirS-VR-RNA regulatory cascade. Several virulence-related genes for alpha-toxin, kappa-toxin, hyaluronidases, sialidase, and capsular polysaccharide synthesis were found. Furthermore, some genes for catalytic enzymes, various genes for transporters, and many genes for energy metabolism were also found to be controlled by the cascade. Our data indicate that the VirR/VirS-VR-RNA system is a global gene regulator that might control multiple cellular functions to survive and multiply in the host, which would turn out to be a lethal flesh-eating infection.

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  • Identification and Classification of a Two-Component System Based on Domain Structures in Bacteria and Differences in Domain Structure between Gram-Positive and Gram-Negative Bacteria

    Kim, S; Hirakawa, H; Muta, S; Kuhara, S

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY   74 ( 4 )   716 - 720   2010.4   ISSN:0916-8451 eISSN:1347-6947

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  • X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils. International journal

    Yukio Yasukochi, Osamu Maruyama, Milind C Mahajan, Carolyn Padden, Ghia M Euskirchen, Vincent Schulz, Hideki Hirakawa, Satoru Kuhara, Xing-Hua Pan, Peter E Newburger, Michael Snyder, Sherman M Weissman

    Proceedings of the National Academy of Sciences of the United States of America   107 ( 8 )   3704 - 3709   2010.2   ISSN:0027-8424

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    The DNA methylation status of human X chromosomes from male and female neutrophils was identified by high-throughput sequencing of HpaII and MspI digested fragments. In the intergenic and intragenic regions on the X chromosome, the sites outside CpG islands were heavily hypermethylated to the same degree in both genders. Nearly half of X chromosome promoters were either hypomethylated or hypermethylated in both females and males. Nearly one third of X chromosome promoters were a mixture of hypomethylated and heterogeneously methylated sites in females and were hypomethylated in males. Thus, a large fraction of genes that are silenced on the inactive X chromosome are hypomethylated in their promoter regions. These genes frequently belong to the evolutionarily younger strata of the X chromosome. The promoters that were hypomethylated at more than two sites contained most of the genes that escaped silencing on the inactive X chromosome. The overall levels of expression of X-linked genes were indistinguishable in females and males, regardless of the methylation state of the inactive X chromosome. Thus, in addition to DNA methylation, other factors are involved in the fine tuning of gene dosage compensation in neutrophils.

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  • A protein secretion system linked to bacteroidete gliding motility and pathogenesis. Reviewed International journal

    Keiko Sato, Mariko Naito, Hideharu Yukitake, Hideki Hirakawa, Mikio Shoji, Mark J McBride, Ryan G Rhodes, Koji Nakayama

    Proceedings of the National Academy of Sciences of the United States of America   107 ( 1 )   276 - 281   2010.1   ISSN:0027-8424

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    Porphyromonas gingivalis secretes strong proteases called gingipains that are implicated in periodontal pathogenesis. Protein secretion systems common to other Gram-negative bacteria are lacking in P. gingivalis, but several proteins, including PorT, have been linked to gingipain secretion. Comparative genome analysis and genetic experiments revealed 11 additional proteins involved in gingipain secretion. Six of these (PorK, PorL, PorM, PorN, PorW, and Sov) were similar in sequence to Flavobacterium johnsoniae gliding motility proteins, and two others (PorX and PorY) were putative two-component system regulatory proteins. Real-time RT-PCR analysis revealed that porK, porL, porM, porN, porP, porT, and sov were down-regulated in P. gingivalis porX and porY mutants. Disruption of the F. johnsoniae porT ortholog resulted in defects in motility, chitinase secretion, and translocation of a gliding motility protein, SprB adhesin, to the cell surface, providing a link between a unique protein translocation system and a motility apparatus in members of the Bacteroidetes phylum.

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    Other Link: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20592142/

  • Identification of the site-specific DNA invertase responsible for the phase variation of SusC/SusD family outer membrane proteins in Bacteroides fragilis. International journal

    Haruyuki Nakayama-Imaohji, Hideki Hirakawa, Minoru Ichimura, Shin Wakimoto, Satoru Kuhara, Tetsuya Hayashi, Tomomi Kuwahara

    Journal of bacteriology   191 ( 19 )   6003 - 6011   2009.10   ISSN:0021-9193 eISSN:1098-5530

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    The human gut microbe Bacteroides fragilis can alter the expression of its surface molecules, such as capsular polysaccharides and SusC/SusD family outer membrane proteins, through reversible DNA inversions. We demonstrate here that DNA inversions at 12 invertible regions, including three gene clusters for SusC/SusD family proteins, were controlled by a single tyrosine site-specific recombinase (Tsr0667) encoded by BF0667 in B. fragilis strain YCH46. Genetic disruption of BF0667 diminished or attenuated shufflon-type DNA inversions at all three susC/susD genes clusters, as well as simple DNA inversions at nine other loci, most of which colocalized with susC/susD family genes. The inverted repeat sequences found within the Tsr0667-regulated invertible regions shared the consensus motif sequence AGTYYYN(4)GDACT. Tsr0667 specifically mediated the DNA inversions of 10 of the 12 regions, even under an Escherichia coli background when the invertible regions were exposed to BF0667 in E. coli cells. Thus, Tsr0667 is an additional globally acting DNA invertase in B. fragilis, which probably involves the selective expression of SusC/SusD family outer membrane proteins.

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  • Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus Reviewed International journal

    Yoshinao Azuma, Akira Hosoyama, Minenosuke Matsutani, Naoko Furuya, Hiroshi Horikawa, Takeshi Harada, Hideki Hirakawa, Satoru Kuhara, Kazunobu Matsushita, Nobuyuki Fujita, Mutsunori Shirai

    NUCLEIC ACIDS RESEARCH   37 ( 17 )   5768 - 5783   2009.9   ISSN:0305-1048 eISSN:1362-4962

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    Acetobacter species have been used for brewing traditional vinegar and are known to have genetic instability. To clarify the mutability, Acetobacter pasteurianus NBRC 3283, which forms a multiphenotype cell complex, was subjected to genome DNA sequencing. The genome analysis revealed that there are more than 280 transposons and five genes with hyper-mutable tandem repeats as common features in the genome consisting of a 2.9-Mb chromosome and six plasmids. There were three single nucleotide mutations and five transposon insertions in 32 isolates from the cell complex. The A. pasteurianus hyper-mutability was applied for breeding a temperature-resistant strain grown at an unviable high-temperature (42 degrees C). The genomic DNA sequence of a heritable mutant showing temperature resistance was analyzed by mutation mapping, illustrating that a 92-kappa b deletion and three single nucleotide mutations occurred in the genome during the adaptation. Alpha-proteobacteria including A. pasteurianus consists of many intracellular symbionts and parasites, and their genomes show increased evolution rates and intensive genome reduction. However, A. pasteurianus is assumed to be a free-living bacterium, it may have the potentiality to evolve to fit in natural niches of seasonal fruits and flowers with other organisms, such as yeasts and lactic acid bacteria.

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  • Structural insight into the binding mode between the targeting domain of ALE-1 (92AA) and pentaglycine of peptidoglycan. Reviewed International journal

    Hideki Hirakawa, Hidenori Akita, Tamaki Fujiwara, Motoyuki Sugai, Satoru Kuhara

    Protein engineering, design & selection : PEDS   22 ( 7 )   385 - 391   2009.7   ISSN:1741-0126 eISSN:1741-0134

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    ALE-1 is a glycylglycine endopeptidase that selectively targets and lyses Staphylococcus aureus, and is expected to be a next generation antibacterial agent because of its substrate specificity to pathogenic bacteria. It has a central catalytic domain and a targeting domain called 92AA. 92AA has been shown to recognize pentaglycine, but the molecular mechanism by which it recognizes and interacts with pentaglycine has not been elucidated. To predict the binding modes of pentaglycine is important for estimating the catalytic reaction mechanism of ALE-1. In the present study, we characterized the binding cleft of 92AA by a computational method and modeled the complexes formed between 92AA and the pentaglycine of peptidoglycan by a binding simulation. In addition, we performed precise simulations of the molecular dynamics by which the complexes identify the amino acid residues interacting with the pentaglycine. We also experimentally constructed mutants in which the amino acid residues present in the binding cleft were changed by site-directed mutagenesis and assessed their ability to bind to peptidoglycan by ELISA. Based on the results of these analyses, we proposed a mode of binding between 92AA and the pentaglycine of peptidoglycan, and modeled the energetically stable complexes between 92AA and the pentaglycine.

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  • Conjugative plasmid pLD-TEX-KL promotes growth of host bacterium Legionella dumoffii at low temperatures. International journal

    Tian Qin, Ken-ichiro Iida, Hideki Hirakawa, Susumu Shiota, Hiroaki Nakayama, Shin-ichi Yoshida

    Archives of microbiology   191 ( 6 )   543 - 551   2009.6   ISSN:0302-8933

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    Legionella (Fluoribacter) dumoffii is a resident of various aquatic environments and occasionally causes pneumonia in humans. We found that L. dumoffii strain TEX-KL carries a 66-kb circular plasmid. As predicted by the presence of tra genes similar to those of other transferable plasmids, we showed that pLD-TEX-KL was actually capable of transferring itself to a plasmid-cured derivative of the original strain. Unexpectedly, this plasmid-free derivative turned out to be partially defective in terms of growth at temperatures 30 degrees C or lower. Subsequent works revealed that the growth defect was attributable to the loss of the plasmid gene traA(Ti) homologous to the traA gene of Ti plasmid from Agrobacterium tumefaciens, and that the growth was restored by the introduction of the mobA/repB gene of plasmid pMMB207. Since the existence of a DNA nickase domain is the only feature common to the traA(Ti) and mobA/repB gene products, we hypothesized that this growth defect at low temperature is related to insufficient DNA transactions, which can somehow be alleviated by the nickase activity of those plasmid-encoded proteins. It was also noted that the above features of growth defect at low temperatures were seen in L. dumoffii cells parasitizing the amebic host Acanthamoeba culbertsoni.

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  • Catalytic reaction mechanism of goose egg-white lysozyme by molecular modelling of enzyme-substrate complex. Reviewed International journal

    Hideki Hirakawa, Atsuko Ochi, Yoshihiro Kawahara, Shunsuke Kawamura, Takao Torikata, Satoru Kuhara

    Journal of biochemistry   144 ( 6 )   753 - 761   2008.12   ISSN:0021-924X eISSN:1756-2651

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    Despite the low similarity between their amino acid sequences, the core structures of the fold between chicken-type and goose-type lysozymes are conserved. However, their enzymatic activities are quite different. Both of them exhibit hydrolytic activities, but the goose-type lysozyme does not exhibit transglycosylation activity. The chicken-type lysozyme has a retaining-type reaction mechanism, while the reaction mechanism of the goose-type lysozyme has not been clarified. To clarify the latter mechanism, goose egg-white lysozyme (GEL)-N-acetyl-D-glucosamine (GlcNAc)6 complexes were modelled and compared with hen egg-white lysozyme (HEL)-(GlcNAc)6 complexes. By systematic conformational search, 48 GEL-(GlcNAc)6 complexes were modelled. The right and left side, and the amino acid residues in subsites E-G were identified in GEL. The GlcNAc residue D could bind towards the right side without distortion and there was enough room for a water molecule to attack the C1 carbon of GlcNAc residue D from alpha-side in the right side and not for acceptor molecule. The result of molecular dynamics simulation suggests that GEL would be an inverting enzyme, and Asp97 would act as a second carboxylate and that the narrow space of the binding cleft at subsites E-G in GEL may prohibit the sugar chain to bind alternative site that might be essential for transglycosylation.

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  • Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis. Reviewed International journal

    Mariko Naito, Hideki Hirakawa, Atsushi Yamashita, Naoya Ohara, Mikio Shoji, Hideharu Yukitake, Keisuke Nakayama, Hidehiro Toh, Fuminobu Yoshimura, Satoru Kuhara, Masahira Hattori, Tetsuya Hayashi, Koji Nakayama

    DNA research : an international journal for rapid publication of reports on genes and genomes   15 ( 4 )   215 - 225   2008.8   ISSN:1340-2838 eISSN:1756-1663

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    The gram-negative anaerobic bacterium Porphyromonas gingivalis is a major causative agent of chronic periodontitis. Porphyromonas gingivalis strains have been classified into virulent and less-virulent strains by mouse subcutaneous soft tissue abscess model analysis. Here, we present the whole genome sequence of P. gingivalis ATCC 33277, which is classified as a less-virulent strain. We identified 2090 protein-coding sequences (CDSs), 4 RNA operons, and 53 tRNA genes in the ATCC 33277 genome. By genomic comparison with the virulent strain W83, we identified 461 ATCC 33277-specific and 415 W83-specific CDSs. Extensive genomic rearrangements were observed between the two strains: 175 regions in which genomic rearrangements have occurred were identified. Thirty-five of those genomic rearrangements were inversion or translocation and 140 were simple insertion, deletion, or replacement. Both strains contained large numbers of mobile elements, such as insertion sequences, miniature inverted-repeat transposable elements (MITEs), and conjugative transposons, which are frequently associated with genomic rearrangements. These findings indicate that the mobile genetic elements have been deeply involved in the extensive genome rearrangement of P. gingivalis and the occurrence of many of the strain-specific CDSs. We also describe here a very unique feature of MITE400, which we renamed MITEPgRS (MITE of P. gingivalis with Repeating Sequences).

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    Other Link: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-20592142/

  • Polymerase chain reaction detection of bacterial 16S rRNA gene in human blood. International journal

    Kosei Moriyama, Chie Ando, Kosuke Tashiro, Satoru Kuhara, Seiichi Okamura, Shuji Nakano, Yasumitsu Takagi, Takeyoshi Miki, Yoshiyuki Nakashima, Hideki Hirakawa

    Microbiology and immunology   52 ( 7 )   375 - 382   2008.7   ISSN:0385-5600 eISSN:1348-0421

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    Bacterial 16S ribosomal RNA genes (rDNA) were detected in blood samples from two healthy individuals by PCR under conditions involving 30 cycles that did not produce any visible products from negative control saline. Even from control samples, PCR involving 35-40 cycles yielded visible bands. Major clones detected in the blood samples, but not in control, were the Aquabacterium subgroup, Stenotrophomonas subgroup, Budvicia subgroup, Serratia subgroup, Bacillus subgroup and Flavobacteria subgroup. No clone was located within the bacteroides-clostridium-lactobacillus cluster, which is indigenous to gastrointestinal flora.

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  • Role of disulfide bonds in goose-type lysozyme. International journal

    Shunsuke Kawamura, Mari Ohkuma, Yuki Chijiiwa, Daiki Kohno, Hiroyuki Nakagawa, Hideki Hirakawa, Satoru Kuhara, Takao Torikata

    The FEBS journal   275 ( 11 )   2818 - 2830   2008.6   ISSN:1742-464X

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    The role of the two disulfide bonds (Cys4-Cys60 and Cys18-Cys29) in the activity and stability of goose-type (G-type) lysozyme was investigated using ostrich egg-white lysozyme as a model. Each of the two disulfide bonds was deleted separately or simultaneously by substituting both Cys residues with either Ser or Ala. No remarkable differences in secondary structure or catalytic activity were observed between the wild-type and mutant proteins. However, thermal and guanidine hydrochloride unfolding experiments revealed that the stabilities of mutants lacking one or both of the disulfide bonds were significantly decreased relative to those of the wild-type. The destabilization energies of mutant proteins agreed well with those predicted from entropic effects in the denatured state. The effects of deleting each disulfide bond on protein stability were found to be approximately additive, indicating that the individual disulfide bonds contribute to the stability of G-type lysozyme in an independent manner. Under reducing conditions, the thermal stability of the wild-type was decreased to a level nearly equivalent to that of a Cys-free mutant (C4S/C18S/C29S/C60S) in which all Cys residues were replaced by Ser. Moreover, the optimum temperature of the catalytic activity for the Cys-free mutant was downshifted by about 20 degrees C as compared with that of the wild-type. These results indicate that the formation of the two disulfide bonds is not essential for the correct folding into the catalytically active conformation, but is crucial for the structural stability of G-type lysozyme.

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  • Genome-wide analysis of Chlamydophila pneumoniae gene expression at the late stage of Infection Reviewed International journal

    Koshiro Miura, Hidehiro Toh, Hideki Hirakawa, Manabu Sugii, Masayuki Murata, Kenta Nakai, Kosuke Tashiro, Satoru Kuhara, Yoshinao Azuma, Mutsunori Shirai

    DNA Research   15 ( 2 )   83 - 91   2008.4   ISSN:1340-2838 eISSN:1756-1663

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    Chlamydophila pneumoniae, an obligate intracellular eubacterium, changes its form from a vegetative reticulate body into an infectious elementary body during the late stage of its infection cycle. Comprehension of the molecular events in the morphological change is important to understand the switching mechanism between acute and chronic infection, which is deemed to relate to the pathogenesis of atherosclerosis. Herein, we have attempted to screen genes expressed in the late stage with a genome-wide DNA microarray, resulting in nomination of 17 genes as the late-stage genes. Fourteen of the 17 genes and six other genes predicted as late-stage genes were confirmed to be up-regulated in the late stage with a quantitative reverse transcriptase-polymerase chain reaction. These 20 late-stage genes were classified into two groups by clustering analysis: 'drastically induced' and 'moderately induced' genes. Out of eight drastically induced genes, four contain sigma(28) promoter-like sequences and the other four contain an upstream common sequence. It suggests that besides sigma(28), there are certain up-regulatory mechanisms at the late stage, which may be involved in the chlamydial morphological change and thus pathogenesis.

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  • Complete genome sequence of Finegoldia magna, an anaerobic opportunistic pathogen Reviewed International journal

    Takatsugu Goto, Atsushi Yamashita, Hideki Hirakawa, Minenosuke Matsutani, Kozo Todo, Kenshiro Ohshima, Hidehiro Toh, Kazuaki Miyamoto, Satoru Kuhara, Masahira Hattori, Tohru Shimizu, Shigeru Akimoto

    DNA Research   15 ( 1 )   39 - 47   2008.2   ISSN:1340-2838 eISSN:1756-1663

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    Finegoldia magna (formerly Peptostreptococcus magnus), a member of the Gram-positive anaerobic cocci (GPAC), is a commensal bacterium colonizing human skin and mucous membranes. Moreover, it is also recognized as an opportunistic pathogen responsible for various infectious diseases. Here, we report the complete genome sequence of F. magna ATCC 29328. The genome consists of a 1,797,577 bp circular chromosome and an 189,163 bp plasmid (pPEP1). The metabolic maps constructed based on the genome information confirmed that most F. magna strains cannot ferment most sugars, except fructose, and have various aminopeptidase activities. Three homologs of albumin-binding protein, a known virulence factor useful for antiphagocytosis, are encoded on the chromosome, and one albumin-binding protein homolog is encoded on the plasmid. A unique feature of the genome is that F. magna encodes many sortase genes, of which substrates may be involved in bacterial pathogenesis, such as antiphagocytosis and adherence to the host cell. The plasmid pPEP1 encodes seven sortase and seven substrate genes, whereas the chromosome encodes four sortase and 19 substrate genes. These plasmid-encoded sortases may play important roles in the pathogenesis of F. magna by enriching the variety of cell wall anchored surface proteins.

    DOI: 10.1093/dnares/dsm030

    Web of Science

    PubMed

  • Evaluating Protein Sequence Signatures Inferred from Protein-Protein Interaction Data by Gene Ontology Annotations.

    Osamu Maruyama, Hideki Hirakawa, Takao Iwayanagi, Yoshiko Ishida, Shizu Takeda, Jun Otomo, Satoru Kuhara

    2008 IEEE International Conference on Bioinformatics and Biomedicine(BIBM)   417 - +   2008   ISSN:2156-1125 ISBN:978-0-7695-3452-7 eISSN:2156-1133

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    Publishing type:Research paper (international conference proceedings)   Publisher:IEEE Computer Society  

    DOI: 10.1109/BIBM.2008.29

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    Other Link: https://dblp.uni-trier.de/db/conf/bibm/bibm2008.html#MaruyamaHIITOK08

  • Complete nucleotide sequence of pLD-TEX-KL, a 66-kb plasmid of <i>Legionella dumoffii</i> TEX-KL strain

    Qin, T; Hirakawa, H; Iida, K; Oshima, K; Hattori, M; Tashiro, K; Kuhara, S; Yoshida, S

    PLASMID   58 ( 3 )   261 - 268   2007.11   ISSN:0147-619X

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  • Enzymatic properties of newly found green turtle egg white ribonuclease

    Katekaew, S; Torikata, T; Hirakawa, H; Kuhara, S; Araki, T

    PROTEIN JOURNAL   26 ( 2 )   75 - 85   2007.2   ISSN:1572-3887 eISSN:1573-4943

  • Construction of enzyme-substrate complexes between hen egg-white lysozyme and <i>N</i>-acetyl-D-glucosamine hexamer by systematic conformational search and molecular dynamics simulation

    Hirakawa, H; Kawahara, Y; Ochi, A; Muta, S; Kawamura, S; Torikata, T; Kuhara, S

    JOURNAL OF BIOCHEMISTRY   140 ( 2 )   221 - 227   2006.8   ISSN:0021-924X

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  • Genome sequence of the cat pathogen, Chlamydophila felis Reviewed International journal

    Yoshinao Azuma, Hideki Hirakawa, Atsushi Yamashita, Yan Cai, Mohd Akhlakur Rahman, Harumi Suzuki, Shigeki Mitaku, Hidehiro Toh, Susumu Goto, Tomoyuki Murakami, Kazuro Sugi, Hideo Hayashi, Hideto Fukushi, Masahira Hattori, Satoru Kuhara, Mutsunori Shirai

    DNA RESEARCH   13 ( 1 )   15 - 23   2006.2   ISSN:1340-2838 eISSN:1756-1663

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:OXFORD UNIV PRESS  

    Chlamydophila felis (Chlamydia psittaci feline pneumonitis agent) is a worldwide spread pathogen for pneumonia and conjunctivitis in cats. Herein, we determined the entire genomic DNA sequence of the Japanese C. felis strain Fe/C-56 to understand the mechanism of diseases caused by this pathogen. The C. felis genome is composed of a circular 1 166 239 bp chromosome encoding 1005 protein-coding genes and a 7552 bp circular plasmid. Comparison of C. felis gene contents with other Chlamydia species shows that 795 genes are common in the family Chlamydiaceae species and 47 genes are specific to C. felis. Phylogenetic analysis of the common genes reveals that most of the orthologue sets exhibit a similar divergent pattern but 14 C. felis genes accumulate more mutations, implicating that these genes may be involved in the evolutional adaptation to the C. felis-specific niche. Gene distribution and orthologue analyses reveal that two distinctive regions, i.e. the plasticity zone and frequently gene-translocated regions (FGRs), may play important but different roles for chlamydial genome evolution. The genomic DNA sequence of C. felis provides information for comprehension of diseases and elucidation of the chlamydial evolution.

    DOI: 10.1093/dnares/dsi027

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    PubMed

  • Whole genome sequence of <i>Staphylococcus saprophyticus</i> reveals the pathogenesis of uncomplicated urinary tract infection

    Kuroda, M; Yamashita, A; Hirakawa, H; Kumano, M; Morikawa, K; Higashide, M; Maruyama, A; Inose, Y; Matoba, K; Toh, H; Kuhara, S; Hattori, M; Ohta, T

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   102 ( 37 )   13272 - 13277   2005.9   ISSN:0027-8424

  • Asp578 in LEU4p is one of the key residues for leucine feedback inhibition release in sake yeast

    Oba, T; Nomiyama, S; Hirakawa, H; Tashiro, K; Kuhara, S

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY   69 ( 7 )   1270 - 1273   2005.7   ISSN:0916-8451 eISSN:1347-6947

  • Genomic analysis of <i>Bacteroides fragilis</i> reveals extensive DNA inversions regulating cell surface adaptation

    Kuwahara, T; Yamashita, A; Hirakawa, H; Nakayama, H; Toh, H; Okada, N; Kuhara, S; Hattori, M; Hayashi, T; Ohnishi, Y

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   101 ( 41 )   14919 - 14924   2004.10   ISSN:0027-8424

  • Bare-faced curassow lysozyme carrying amino acid substitutions at subsites E and F shows a change in activity against chitooligosaccharide caused by a local conformational change. International journal

    Tomohiro Araki, Shinobu Seki, Hideki Hirakawa, Yuki Chijiiwa, Shunsuke Kawamura, Satoru Kuhara, Takao Torikata

    Journal of biochemistry   136 ( 4 )   485 - 93   2004.10   ISSN:0021-924X

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    Language:English   Publishing type:Research paper (scientific journal)  

    A new form of avian lysozyme, bare-faced curassow lysozyme (BCL), was purified and chemically sequenced. Of the 26 substitutions relative to chicken lysozyme, three, F34Y, T47S, and R114H, are of substrate-interacting residues in the E and F subsites, which would contribute to the acceptor binding for transglycosylation. T47S is a novel substitution in this lysozyme class. While other lysozymes also have substitutions at positions 114 and 34, they also contain numerous others, including ones in the other substrate binding sites, A-D. Furthermore, T47S lies on the left side, while F34Y and R114H are located on the right side of the E-F subsites. BCL therefore should allow comparison of the independent contributions of these sites to substrate binding and transglycosylation. The activity toward the N-acetylglucosamine pentamer revealed that the substitutions at the E-F sites reduced the binding free energies at the E-F sites and the rate constant for transglycosylation without the conformation change of other substrate binding sites on the protein. MD simulation analysis of BCL suggested that the substituted amino acids changed the local conformation of this lysozyme at the E-F sites.

    PubMed

  • Heterogeneity of <i>dnaB</i> locus of <i>Mycobacterium avium-intracellulare</i> complex

    Yamamoto, K; Rutherford, SA; Rajagopalan, M; Hirakawa, H; Kuhara, S; Banno, Y; Fujii, H; Madiraju, MVVS

    JOURNAL OF THE FACULTY OF AGRICULTURE KYUSHU UNIVERSITY   49 ( 2 )   375 - 381   2004.10   ISSN:0023-6152

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  • Furin-like proprotein convertase from the silkworm, <i>Bombyx mori</i>:: cDNA and its baculoviral expression

    Aso, Y; Iwashita, T; Yamagami, T; Yamamoto, K; Hirakawa, H; Ishino, Y; Fujii, H

    PROTEIN SCIENCE   13   142 - 142   2004.8   ISSN:0961-8368

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  • Nucleotide substitutions in <i>Staphylococcus aureus</i> strains, Mu50, Mu3, and N315

    Ohta, T; Hirakawa, H; Morikawa, K; Maruyama, A; Inose, Y; Yamashita, A; Oshima, K; Kuroda, M; Hattori, M; Hiramatsu, K; Kuhara, S; Hayashi, H

    DNA RESEARCH   11 ( 1 )   51 - 56   2004.2   ISSN:1340-2838

  • Amino acid residue substitution at T-cell determinant-flanking sites in β-lactoglobulin modulates antigen presentation to T cells through subtle conformational change

    Ametani, A; Sakurai, T; Katakura, Y; Kuhara, S; Hirakawa, H; Hosoi, T; Dosako, SI; Kaminogawa, S

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY   67 ( 7 )   1507 - 1514   2003.7   ISSN:0916-8451 eISSN:1347-6947

  • Mutational analysis of amino acid residues involved in catalytic activity of a family 18 chitinase from tulip bulbs

    Suzukawa, K; Yamagami, T; Ohnuma, T; Hirakawa, H; Kuhara, S; Aso, Y; Ishiguro, M

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY   67 ( 2 )   341 - 346   2003.2   ISSN:0916-8451 eISSN:1347-6947

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  • Comparative DNA sequence analysis of mouse and human CC chemokine gene clusters. International journal

    Hisayuki Nomiyama, Kimie Egami, Sumio Tanase, Retsu Miura, Hideki Hirakawa, Satoru Kuhara, Jun Ogasawara, Shinichi Morishita, Osamu Yoshie, Jun Kusuda, Katsuyuki Hashimoto

    Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research   23 ( 1 )   37 - 45   2003.1   ISSN:1079-9907

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    Language:English   Publishing type:Research paper (scientific journal)  

    The CC chemokines are a closely related subfamily of the chemokine superfamily. Most of the CC chemokine genes form a cluster on chromosome 11 in mice and chromosome 17 in humans. To date, 11 and 16 functional genes have been localized within the mouse and human clusters, respectively. Notably, some of the genes within these clusters appear to have no counterparts between the two species, and the orthologous relationships of some of the genes are difficult to establish solely on the basis of amino acid similarity. In this study, we have taken a comparative genomic approach to reveal some of the features that may be involved in the dynamic evolution of these gene clusters. We sequenced a 122-kb region containing five chemokine genes of the mouse CC cluster. This mouse sequence was combined with those determined by the Mouse Genome Sequencing Project, and the entire sequence of the mouse CC cluster was compared with that of the corresponding cluster in the human genome by percent identity plot and dot-plot analyses. Although no additional chemokine genes have been found in these clusters, our analysis has revealed that numerous gene rearrangements have occurred even after the diversification of rodents and primates, resulting in several species-specific chemokine genes and pseudogenes. In addition, phylogenetic analysis and comparison of the genomic sequences unambiguously identified the orthologous relationships of some of the chemokine genes in the mouse and human CC gene clusters.

    PubMed

  • Complete genome sequence of <i>Clostridium perfringens</i>, an anaerobic flesh-eater

    Shimizu, T; Ohtani, K; Hirakawa, H; Ohshima, K; Yamashita, A; Shiba, T; Ogasawara, N; Hattori, M; Kuhara, S; Hayashi, H

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   99 ( 2 )   996 - 1001   2002.1   ISSN:0027-8424

  • Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. International journal

    Tohru Shimizu, Kaori Ohtani, Hideki Hirakawa, Kenshiro Ohshima, Atsushi Yamashita, Tadayoshi Shiba, Naotake Ogasawara, Masahira Hattori, Satoru Kuhara, Hideo Hayashi

    Proceedings of the National Academy of Sciences of the United States of America   99 ( 2 )   996 - 1001   2002.1   ISSN:0027-8424

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    Language:English   Publishing type:Research paper (scientific journal)  

    Clostridium perfringens is a Gram-positive anaerobic spore-forming bacterium that causes life-threatening gas gangrene and mild enterotoxaemia in humans, although it colonizes as normal intestinal flora of humans and animals. The organism is known to produce a variety of toxins and enzymes that are responsible for the severe myonecrotic lesions. Here we report the complete 3,031,430-bp sequence of C. perfringens strain 13 that comprises 2,660 protein coding regions and 10 rRNA genes, showing pronounced low overall G + C content (28.6%). The genome contains typical anaerobic fermentation enzymes leading to gas production but no enzymes for the tricarboxylic acid cycle or respiratory chain. Various saccharolytic enzymes were found, but many enzymes for amino acid biosynthesis were lacking in the genome. Twenty genes were newly identified as putative virulence factors of C. perfringens, and we found a total of five hyaluronidase genes that will also contribute to virulence. The genome analysis also proved an efficient method for finding four members of the two-component VirR/VirS regulon that coordinately regulates the pathogenicity of C. perfringens. Clearly, C. perfringens obtains various essential materials from the host by producing several degradative enzymes and toxins, resulting in massive destruction of the host tissues.

    PubMed

  • Whole genome sequencing of meticillin-resistant Staphylococcus aureus

    Makoto Kuroda, Toshiko Ohta, Ikuo Uchiyama, Tadashi Baba, Harumi Yuzawa, Ichizo Kobayashi, Longzhu Cui, Akio Oguchi, Ken-ichi Aoki, Yoshimi Nagai, JianQi Lian, Teruyo Ito, Mutsumi Kanamori, Hiroyuki Matsumaru, Atsushi Maruyama, Hiroyuki Murakami, Akira Hosoyama, Yoko Mizutani-Ui, Noriko K Takahashi, Toshihiko Sawano, Ryu-ichi Inoue, Chikara Kaito, Kazuhisa Sekimizu, Hideki Hirakawa, Satoru Kuhara, Susumu Goto, Junko Yabuzaki, Minoru Kanehisa, Atsushi Yamashita, Kenshiro Oshima, Keiko Furuya, Chie Yoshino, Tadayoshi Shiba, Masahira Hattori, Naotake Ogasawara, Hideo Hayashi, Keiichi Hiramatsu

    The Lancet   357 ( 9264 )   1225 - 1240   2001.4   ISSN:0140-6736

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    Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/S0140-6736(00)04403-2

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    PubMed

  • Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA Reviewed

    Mutsunori Shirai, Hideki Hirakawa, Mitsuaki Kimoto, Mitsuaki Tabuchi, Fumio Kishi, Kazunobu Ouchi, Tadayoshi Shiba, Kazuo Ishii, Masahira Hattori, Satoru Kuhara, Teruko Nakazawa

    Nucleic Acids Research   28 ( 12 )   2311 - 2314   2000.6   ISSN:0305-1048

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    Language:English   Publishing type:Research paper (scientific journal)  

    Chlamydia pneumoniae is a widespread pathogen of humans causing pneumonia and bronchitis. There are many reports of an association between C. pneumoniae infection and atherosclerosis. We determined the whole genome sequence of C. pneumoniae strain J138 isolated in Japan in 1994 and compared it with the sequence of strain CWL029 isolated in the USA before 1987. The J138 circular chromosome consists of 1,226,565 nt (40.7% G + C) with 1072 likely protein-coding genes that is 3665 nt shorter than the CWL029 genome. Plasmids, phage- or transposon-like sequences were not identified. The overall genomic organization, gene order and predicted proteomes of the two strains are very similar, suggesting a high level of structural and functional conservation between the two unrelated isolates. The most conspicuous differences in the J138 genome relative to the CWL029 genome are the absence of five DNA segments, ranging in size from 89 to 1649 nt, and the presence of three DNA segments, ranging from 27 to 84 nt. The complex organization of these 'different zones' may be attributable to a unique system of recombination.

    Scopus

    PubMed

  • Comparision of outer membrane protein genes omp and pmp in the whole genome sequences of Chlamydia pneumoniae isolates from Japan and the United States

    SHIRAI M

    J Infect Dis   181   S524 - S527   2000.6   ISSN:0022-1899 eISSN:1537-6613

  • The hydrophobic cores of proteins predicted by wavelet analysis

    H. Hirakawa, S. Muta, S. Kuhara

    Bioinformatics   15 ( 2 )   141 - 148   1999.2   ISSN:1367-4803

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    Language:English   Publishing type:Research paper (scientific journal)  

    Motivation: In the process of protein construction, buried hydrophobic residues tend to assemble in a core of a protein. Methods used to predict these cores involve use or no use of sequential alignment. In the case of a close homology, prediction was more accurate if sequential alignment was used. If the homology was weak, prediction would be unreliable. A hydrophobicity plot involving the hydropathy index is useful for purposes of prediction, and smoothing is essential. However, the proposed methods are insufficient. We attempted to predict hydrophobic cores with a low frequency extracted from the hydrophobicity plot, using wavelet analysis. Results: The cores were predicted at a rate of 68.7%, by cross-validation. Using wavelet analysis, the cores of non-homologus proteins can be predicted with close to 70% accuracy, without sequential alignment. Availability: The program used in this study is available from Interglactic Reality (http://www.intergalact.com).

    DOI: 10.1093/bioinformatics/15.2.141

    Web of Science

    Scopus

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Presentations

  • 菌根菌叢・細菌叢同定ウェブインターフェースの開発

    平川 英樹, 丹羽理恵子, 佐藤修正, 江沢辰広

    第17回 日本ゲノム微生物学会年会  2023.3 

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    Language:Japanese   Presentation type:Poster presentation  

MISC

  • Improvement of Plant GARDEN, a portal site for plant genome information (FY2023, Q4 ver): Development of tools to use evolutionary information

    市原寿子, 山田学, 戸田陽介, 中谷明弘, 山下サマッチャヤー, 清水武彦, 白澤沙知子, 小原光代, 平川英樹, 中村保一, 中村保一, 七夕高也, 田畑哲之, 磯部祥子

    育種学研究   26   2024   ISSN:1344-7629

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  • Development of waxy common buckwheat using NGS-TILLING

    安井康夫, FAWCETT J., 田中朋之, 西村和紗, 西村和紗, 中崎鉄也, 岩橋優, 齊藤大樹, 竹内直子, 上野まりこ, 上野まりこ, 白澤健太, 平川英樹, 大田竜也

    育種学研究   25   2023   ISSN:1344-7629

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  • GRAS-Di技術を用いたコウヨウザンの連鎖地図構築とQTL解析

    平尾知士, 藤澤義武, 白澤健太, 武津英太郎, 平川英樹, 三嶋賢太郎, 磯田圭哉, 山田浩雄

    日本森林学会大会学術講演集   134th   2023   ISSN:2187-6576

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  • カラマツ雄花と雌花からの発現遺伝子の取得と着花に関わる遺伝子座の探索

    三嶋賢太郎, 井城泰一, 平川英樹, 白澤健太, 福田陽子, 福田有樹, 宮本尚子, 平尾知士, 永野聡一郎, 小長谷賢一, 平岡裕一郎, 田村明, 倉本哲嗣, 高橋誠

    日本森林学会大会学術講演集   134th   2023   ISSN:2187-6576

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  • Genome sequencing reveals the genetic architecture of heterosytly in common buckwheat

    FAWCETT Jeffrey, 竹島亮馬, 松井勝弘, 水野信之, 松本大生, 平川英樹, 大田竜也, 安井康夫

    日本遺伝学会大会プログラム・予稿集   95th (CD-ROM)   2023

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  • Gene Cluster CqCYP76AD1 and CqDODA1 Regulating Betalain Production in Quinoa

    久篠沙耶子, 水野信之, 西村和紗, 上野まりこ, 中崎鉄也, 小林安文, 藤田泰成, 白澤健太, 平川英樹, 安井康夫, 桂圭佑

    日本作物学会講演会要旨集   256th   2023

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  • Quinoa: an emerging model experimental plant with high nutritional value and adaptability to harsh environments

    藤田泰成, 藤田泰成, 豊島真実, 小林安文, 藤田美紀, 小賀田拓也, 白澤健太, 平川英樹, 永利友佳理, 安井康夫

    日本分子生物学会年会プログラム・要旨集(Web)   46th   2023

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  • Characterization of MYB transcripts in epigenetic regulated variegated petals of Saintpaulia

    倉田大地, 平川英樹, 白澤健太, 立澤文見, 細川宗孝, 細川宗孝

    園芸学研究 別冊   22 ( 1 )   2023   ISSN:1881-8307

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  • Buckwheat genome project-outline and perspectives-

    大田竜也, FAWCETT J., 竹島亮馬, 菊池真司, 大迫敬義, 白澤健太, 法月美悠, 松井勝弘, 矢崎裕規, 木曽映里, 藤井健一郎, 原尚資, JONES Martin K., 平川英樹, LI Cheng-Yun, 安井康夫

    育種学研究   25   2023   ISSN:1344-7629

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  • Flavonoid biosynthesis and regulatory system revealed by genome sequencing in buckwheat

    松井勝弘, 大島良美, 光田展隆, 坂本真吾, FAWCETT J., 平川英樹, 大田竜也, 安井康夫

    育種学研究   25   2023   ISSN:1344-7629

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  • Genetic architecture of heteromorphic self-incompatibility in common buckwheat

    竹島亮馬, FAWCETT J., 松井勝弘, 水野信之, 松本大生, 平川英樹, 大田竜也, 安井康夫

    育種学研究   25   2023   ISSN:1344-7629

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  • Exploration of Flowering Regulator Genes in Swertia japonica Makino (3)

    河野徳昭, 平川英樹, 山本和彦, 熊谷健夫, 渕野裕之, 川原信夫, 川原信夫, 由井秀紀, 金子倫久, 高田泰生, 吉松嘉代

    日本薬学会年会要旨集(Web)   143rd   2023   ISSN:0918-9823

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  • The changes of expression level of ERF transcription factors during cold acclimation in Saintpaulia

    福富健人, 倉田大地, 平川英樹, 白澤健太, 久保香奈衣, 細川宗孝, 細川宗孝, 細川宗孝

    園芸学研究 別冊   22 ( 1 )   2023   ISSN:1881-8307

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  • Hemizygous Genomic Region Controls Distyly in Buckwheat-It Isn’t the Classical Super Gene Model-

    安井康夫, 竹島亮馬, FAWCETT Jeffrey, 松井勝弘, 水野信之, 松本大生, 平川英樹, 白澤健太, 大田竜也

    日本分子生物学会年会プログラム・要旨集(Web)   46th   2023

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  • ロングリード技術による針葉樹4種の全ゲノム解読

    白澤健太, 三嶋賢太郎, 平川英樹, 平尾知士, 坪村美代子, 永野聡一郎, 井城泰一, 磯部祥子, 高橋誠

    日本森林学会大会学術講演集   134th   2023   ISSN:2187-6576

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  • Comparative genomic analysis of 25 peach cultivars

    衣川達己, 谷澤靖洋, 中村保一, 伊藤武彦, 田中裕之, 平川英樹, 篠澤章久, 篠澤章久, 馬場正, 小田賢司, 井出大輔, 大和勝幸, 石丸恵

    園芸学研究 別冊   22 ( 1 )   2023   ISSN:1881-8307

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  • Genetics and Genomics of Orphan Crops and their perspectives

    大田竜也, FAWCETT Jeffrey A., 竹島亮馬, 菊池真司, 大迫敬義, 白澤健太, 法月美悠, 松井勝弘, 矢崎裕規, 小木曽映里, 藤井健一郎, 原尚資, JONES Martin K., 平川英樹, LI Cheng-Yun, 安井康夫

    日本進化学会大会プログラム・講演要旨集(Web)   25th   2023

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  • Improvement of Plant GARDEN, a portal site for plant genome information (2023, Q2 ver)

    市原寿子, 小原光代, 山下サマッチャヤー, 山田学, 清水武彦, 白澤沙知子, 戸田陽介, 平川英樹, 中村保一, 中村保一, 七夕高也, 田畑哲之, 磯部祥子

    育種学研究   25   2023   ISSN:1344-7629

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  • Improvement of a plant genome information portal site, Plant GARDEN (2022, Q4 ver)

    市原寿子, 平川英樹, 山田学, 小原光代, 山下サマッチャヤー, 白澤沙知子, 戸田陽介, 清水武彦, 中村保一, 中村保一, 七夕高也, 田畑哲之, 磯部祥子

    育種学研究   25   2023   ISSN:1344-7629

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  • Response of non-leguminous plants during rhizobium inoculation

    梅月毬華, 下田宜司, 磯部祥子, 花野滋, 平川英樹, 富永晃好, 壽崎拓哉, 征矢野敬, 川口正代司, 佐藤修正, 内海俊樹

    植物微生物研究会研究交流会講演要旨集   32nd   2023   ISSN:1341-0652

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  • Pan genome of strawberry varieties in Japan

    磯部祥子, 白澤健太, 平川英樹, 濱野恵, 龍勝利, 黒倉健

    園芸学研究 別冊   22 ( 1 )   2023   ISSN:1881-8307

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  • 針葉樹4種のゲノム情報データベースBreeding Trees-by-Genesの構築

    平川英樹, 白澤健太, 井城泰一, 高島有哉, 福田有樹, 平尾知士, 三嶋賢太郎

    日本森林学会大会学術講演集   134th   2023   ISSN:2187-6576

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  • 【バイオDBとウェブツール ラボで使える最新70選 知る・学ぶ・使う、バイオDX時代の羅針盤】(第3章)ゲノム・遺伝子・NGSデータを調べる ゲノム Plant GARDEN さまざまな植物のゲノムやマーカー情報を集めたポータルサイト

    磯部 祥子, 市原 寿子, 平川 英樹

    実験医学   40 ( 17 )   2774 - 2776   2022.11   ISSN:0288-5514

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  • MicrobeDB.jpからMicrobiome Datahubへ: 微生物・植物・メタボロームのデータ統合と統合微生物データベースの再構築

    藤澤 貴智, 平川 英樹, 守屋 勇樹, 信定 知江, 金谷 重彦, 有田 正規, 田畑 哲之, 磯部 祥子, 東 光一, 中村 保一, 松井 求, 山田 拓司, 内山 郁夫, 黒川 顕, 森 宙史

    トーゴーの日2022   1   2022.10

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    Publisher:JST NBDC事業推進部  

    DOI: 10.18908/togo2022.p010

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  • Improvement of Plant GARDEN, a portal site for plant genome information (2022, Q2 ver)

    市原寿子, 平川英樹, 山田学, 小原光代, 山下サマッチャヤー, 白澤沙知子, 戸田陽介, 中村保一, 中村保一, 七夕高也, 田畑哲之, 磯部祥子

    育種学研究   24   1   2022.10   ISSN:1344-7629

  • 植物ゲノム統合データベースPlant GARDEN、微生物、メタボローム統合データベース間の連携検索システムの開発

    平川 英樹, 藤澤 貴智, 守屋 勇樹, 信定 知江, 長崎 英樹, 森 宙史, 福島 敦史, Ghelfi Andrea, 市原 寿子, 中村 保一, 金谷 重彦, 有田 正規, 黒川 顕, 田畑 哲之, 磯部 祥子

    トーゴーの日2022   1   2022.10

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    DOI: 10.18908/togo2022.p016

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  • Identification of genes associated with red pigment production in quinoa true leaves using <i>de novo</i> assembly and bulked segregant analysis

    Kushino Sayako, Mizuno Nobuyuki, Nishimura Kazusa, Ueno Mariko, Nakazaki Tetsuya, Kobayashi Yasufumi, Fujita Yasunari, Shirasawa Kenta, Hirakawa Hideki, Yasui Yasuo, Katsura Keisuke

    Abstracts of Meeting of the CSSJ   254   70 - 70   2022.9

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    Language:Japanese   Publisher:CROP SCIENCE SOCIETY OF JAPAN  

    DOI: 10.14829/jcsproc.254.0_70

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  • De novo genome assembly of ‘Shine Muscat’ and a SNP panel construction by using re-sequencing data of grapevine varieties

    磯部祥子, 白澤健太, 谷口郁也, 平川英樹, 山本俊哉, 佐藤明彦, 佐藤明彦, 東暁史

    園芸学研究 別冊   21 ( 2 )   2022   ISSN:1881-8307

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  • Plant GARDENからMi-GARDENへ~公開ゲノム情報とユーザーデータをつなぐ~

    磯部祥子, 市原寿子, 山田学, 中村保一, 中村保一, 戸田陽介, 小原光代, 山下サマッチャヤー, 七夕高也, 平川英樹, 田畑哲之

    日本植物学会大会研究発表記録(CD-ROM)   86th   2022

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  • MetaboBank: repository of raw data and related resources for metabolome research

    時松敏明, 児玉悠一, 福田亜沙美, 藤澤貴智, 長崎英樹, 荒武, 荒武, 高橋みき子, 大澤祥子, 小林紀郎, 櫻井望, 福島敦史, 福島敦史, 金谷重彦, 平川英樹, 有田正規, 有田正規

    質量分析総合討論会講演要旨集   70th   2022

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  • カラマツ着花変異系統を用いた着花に関わる原因遺伝子座の探索

    三嶋賢太郎, 井城泰一, 平川英樹, 白澤健太, 福田陽子, 福田有樹, 宮本尚子, 平尾知士, 永野聡一郎, 平岡裕一郎, 田村明, 倉本哲嗣, 高橋誠

    日本森林学会大会学術講演集   133rd   2022   ISSN:2187-6576

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  • ゲノム・遺伝子・NGSデータを調べる ゲノム 4.Plant GARDEN-さまざまな植物のゲノムやマーカー情報を集めたポータルサイト

    磯部祥子, 市原寿子, 平川英樹

    実験医学   40 ( 17 )   2022   ISSN:0288-5514

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  • Reduced expression of FNS II in a low-anthocyanin content mutant of Saintpaulia ‘Kilauea’

    倉田大地, 笹部由梨, 津崎智久, 立澤文見, 平川英樹, 白澤健太, 細川宗孝, 細川宗孝

    園芸学研究 別冊   21 ( 1 )   2022   ISSN:1881-8307

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  • Exploration of Flowering Regulator Genes in Swertia japonica Makino

    河野徳昭, 平川英樹, 山本和彦, 熊谷健夫, 渕野裕之, 川原信夫, 川原信夫, 由井秀紀, 金子倫久, 高田泰生, 吉松嘉代

    日本薬学会年会要旨集(Web)   142nd   2022   ISSN:0918-9823

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  • Regional expression of different MYB transcription factors in white-striped petals of Saintpaulia

    倉田大地, 津崎智久, 立澤文見, 平川英樹, 白澤健太, 細川宗孝, 細川宗孝

    園芸学研究 別冊   21 ( 2 )   2022   ISSN:1881-8307

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  • Expression of ethylene-related genes during low temperature acclimatization in Saintpaulia

    福富健人, 倉田大地, 平川英樹, 白澤健太, 久保香奈衣, 細川宗孝, 細川宗孝, 細川宗孝

    園芸学研究 別冊   21 ( 2 )   2022   ISSN:1881-8307

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  • QTL analysis of femaleness in monoecious spinach

    山野薫, 豊田敦, 平川英樹, 小野寺康之

    育種学研究   24   2022   ISSN:1344-7629

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  • Widespread LTR retrotransposon activation in inter- and intra-species recombinant inbred populations of Lotus japonicus

    深井英吾, 深井英吾, 深井英吾, 深井英吾, 深井英吾, 吉川学, SHAH N., SANDAL N., 宮尾安藝雄, 小野聖二郎, 平川英樹, AKYOL T., 梅原洋佐, 野々村賢一, STOUGAARD J., 廣近洋彦, 林誠, 林誠, 佐藤修正, 佐藤修正, ANDERSEN S., 岡崎桂一

    育種学研究   24   2022   ISSN:1344-7629

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  • QTL analysis of femaleness in monoecious spinach by using chromosome-scale pseudomolecules

    Yamano K, Toyoda A, Hirakawa H, Onodera Y

    Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan   63   48 - 49   2022   eISSN:2432-0307

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    Language:Japanese   Publisher:Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  

    DOI: 10.20751/hdanwakai.63.0_48

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  • Improvement of a plant genome information portal site, Plant GARDEN (2021・Q4 ver)

    市原寿子, 平川英樹, GHELFI A., 小原光代, 山田学, 田村卓郎, 中谷明弘, 中村保一, 白澤沙知子, 杉原英志, 田畑哲之, 磯部祥子

    育種学研究   24   2022   ISSN:1344-7629

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  • What genome analysis reveals for understanding plant diversity

    磯部祥子, 白澤健太, 佐藤光彦, 市原寿子, 田島直之, 平川英樹

    育種学研究   24   2022   ISSN:1344-7629

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  • Mi-GARDEN: A platform for comparison of user’s genome sequence data and reference genomes in plants

    磯部祥子, 堀口晃一郎, 山田学, 三澤拓真, 中村保一, 市原寿子, 小原光代, 平川英樹

    育種学研究   24   2022   ISSN:1344-7629

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  • 未利用地から農地への転換に伴う土壌微生物群集構造変化の解析

    高田理江, 花野滋, 宮本託志, 滝澤理仁, 冨永逹, 柴田大輔, 櫻井望, 平川英樹, 小林優

    日本土壌肥料学会講演要旨集(Web)   68   2022   ISSN:2424-0575

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  • Cats’-I: The Genome Information Database of the Novel Domestic Cat Genome Assembly AnAms1.0

    坂本美佳, 松本悠貴, 磯部祥子, CHUNG Claire, LIN Xiao, CHAN Ting-Fung, 平川英樹, 石原玄基, LAM Hon-Ming, 中山しのぶ, 笹本茂美, 谷澤靖洋, 渡辺安希子, 渡部桂, 矢倉勝, 中村保一

    日本分子生物学会年会プログラム・要旨集(Web)   44th   2021

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  • Comparative analysis of sex chromosomes in Spinacia species

    小野寺康之, 藤田拓希, 杉山優, 豊田敦, 平川英樹

    育種学研究   23   2021   ISSN:1344-7629

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  • De novo assembly of the strawberry genomes by using Hifi reads

    磯部祥子, 白澤健太, 平川英樹, 外西萌梨, 濱野恵, 龍勝利, 黒倉健

    園芸学研究 別冊   20 ( 2 )   2021   ISSN:1881-8307

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  • イエネコの高精度な参照ゲノム配列AnAms1.0の構築

    松本悠貴, 磯部祥子, 坂本美佳, CHUNG Claire, CHAN Ting-Fung, 平川英樹, 石原玄基, LAM Hon-Ming, 中山しのぶ, 笹本茂美, 谷沢靖洋, 渡辺安希子, 渡部桂, 矢倉勝, 中村保一

    日本哺乳類学会大会プログラム・講演要旨集   2021   2021

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  • Whole genome sequencing of the model strain Gojo-0 and application to positional cloning in Chrysanthemum

    中野道治, 平川英樹, 豊田敦, 伊藤武彦, 白澤健太, 磯部祥子, 谷口研至, 草場信

    園芸学研究 別冊   20 ( 1 )   2021   ISSN:1881-8307

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  • Whole genome sequencing of the model strain Gojo-O and construction of molecular genetic basis in Chrysanthemum

    中野道治, 平川英樹, 豊田敦, 伊藤武彦, 白澤健太, 磯部祥子, 谷口研至, 草場信

    育種学研究   23   2021   ISSN:1344-7629

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  • カラマツとグイマツの完全長cDNA配列の取得と種間比較

    三嶋賢太郎, 平川英樹, 井城泰一, 福田陽子, 平尾知士, 田村明, 高橋誠

    日本森林学会大会学術講演集   132nd   2021   ISSN:2187-6576

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  • Prediction of flavonoid biosynthesis pathway in Saintpaulia based on whole genome and UniGene data

    倉田大地, 津崎智久, 平川英樹, 白澤健太, 立澤文見, 細川宗孝, 細川宗孝

    園芸学研究 別冊   20 ( 2 )   2021   ISSN:1881-8307

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  • Genetic analysis of inbreeding depression on abnormal leaf shape in common buckwheat

    竹島亮馬, 安井康夫, 平川英樹, 松井勝弘

    育種学研究   23   2021   ISSN:1344-7629

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  • De novo genome assembly of pea (Pisum sativum) with nanopore sequencing technology

    白澤健太, 佐々木和浩, 佐々木和浩, 平川英樹, 磯部祥子

    育種学研究   23   2021   ISSN:1344-7629

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  • De novo whole genome assembly in hexaploid sweetpotato, ‘Xushu 18’

    磯部祥子, 白澤健太, 平川英樹, 田中勝, 高畑康浩, YOON Ung-Han, YOON Ung-Han, CAO Qinghe, LIU Qingchan, ZAI Hong, KWAK Sang-Soo, KWAK Sang-Soo, MA Daifu

    育種学研究   23   2021   ISSN:1344-7629

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  • Whole-genome resequencing of Japanese tomato cultivars provides insights into the history of modern breeding

    山本英司, 松永啓, 大山暁男, 布目司, 白澤健太, 平川英樹, 磯部祥子

    育種学研究   23   2021   ISSN:1344-7629

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  • Multi-omics driven approach explores the evolution of specialized metabolites in plants

    RAI Amit, HIRAKAWA Hideki, NAKABAYASHI Ryo, KIKUCHI Shinji, HAYASHI Koki, RAI Megha, TSUGAWA Hiroshi, MORI Tetsuya, YAMAZAKI Mami, SAITO Kazuki

    質量分析総合討論会講演要旨集   69th   2021

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  • マツ材線虫病に対する抵抗性の遺伝領域を明らかにする

    平尾知士, 松永孝治, 平川英樹, 白澤健太, 磯田圭哉, 三嶋賢太郎, 田村美帆, 渡辺敦史

    森林総合研究所中長期計画成果集   2021

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  • 大規模データ時代のDBの役割は?~Plant GARDENの開発現場から~

    磯部祥子, 市原寿子, 七夕高也, ジェルフィ アンドレア, 兒玉晋洋, 小原光代, 山田学, 白澤沙知子, 田村卓郎, 杉原英志, 中村保一, 中谷明弘, 平川英樹, 田畑哲之

    日本植物学会大会研究発表記録(CD-ROM)   85th   2021

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  • Application of plant metabolome metadata to RDF and reanalysis of the raw data

    長崎英樹, 荒武, 福島敦史, 大澤祥子, 高橋みき子, 小林紀郎, 藤澤貴智, 櫻井望, 平川英樹, 有田正規, 有田正規

    日本植物生理学会年会(Web)   62nd   2021

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  • Improvement of a plant genome information portal site, Plant GARDEN (2020, Q4 ver)

    市原寿子, 小原光代, 山田学, GHELFI A., 平川英樹, 白澤沙知子, 田村卓郎, 杉原英志, 中村保一, 中谷明弘, 田畑哲之, 磯部祥子

    育種学研究   23   2021   ISSN:1344-7629

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  • How to use the plant genome portal site “Plant GARDEN

    市原寿子, 平川英樹, GHELFI Andrea, 小原光代, 山田学, 田村卓郎, 中谷明弘, 中村保一, 白澤沙智子, 杉原英志, 田畑哲之, 磯部祥子

    日本分子生物学会年会プログラム・要旨集(Web)   44th   2021

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  • Genome features of common vetch (Vicia sativa) in natural habitats provide an insight into new plant domestication

    白澤健太, 小杉俊一, 小杉俊一, 佐々木和浩, 佐々木和浩, GHELFI A., GHELFI A., 岡崎孝映, 豊田敦, 平川英樹, 磯部祥子

    育種学研究   23   2021   ISSN:1344-7629

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  • Transcriptome analysis of the defense-associated genes in the bacterial canker-infected tomato tissue by RNA-Seq

    横谷尚起, 長谷川嘉則, 香西雄介, 山本英司, 平川英樹, 内藤嘉磯

    日本植物病理学会大会プログラム・講演要旨予稿集   2020   2020

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  • Genome sequencing of Hydrangea macrophylla and DNA marker development for double flower phenotype

    奈島賢児, 白澤健太, 平川英樹, 磯部祥子, 巣山拓郎, 和田卓也, 黒倉健, 上町達也, 東未来, 阿久津翠, 中澤佳子, 小玉雅晴, 生井潔

    園芸学研究 別冊   19 ( 1 )   2020   ISSN:1881-8307

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  • クロマツの連鎖地図構築とマツ材線虫病抵抗性に関する主要遺伝子座の同定

    平尾知士, 松永孝治, 平川英樹, 白澤健太, 磯田圭哉, 三嶋賢太郎, 田村美帆, 渡辺敦史

    日本森林学会大会学術講演集   131st   2020   ISSN:2187-6576

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  • ゲノムワイドアソシエーション解析(GWAS)によるカラマツ材質に関わる遺伝子座の同定

    三嶋賢太郎, 平尾知士, 田村明, 福田有樹, 平岡裕一郎, 井城泰一, 福田陽子, 花岡創, 高島有哉, 谷口亨, 中田了五, 藤原健, 倉本哲嗣, 高橋誠, 平川英樹

    日本木材学会大会研究発表要旨集(完全版)(CD-ROM)   70th   2020   ISSN:1349-0532

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  • Raphanus sativus Genome DataBase

    平川英樹, 白澤健太, 板橋悦子, 吹野伸子, 北柴大泰

    育種学研究   22   2020   ISSN:1344-7629

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  • Characterization of candidate genes for dioecism and monoecism in spinach.

    小野寺康之, 須藤有紀, 平川英樹, 鈴木穣

    園芸学研究 別冊   19 ( 1 )   2020   ISSN:1881-8307

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  • 二倍体野生種のゲノム情報を利用したキクDNAマーカーの効率的な開発技術

    住友克彦, 白澤健太, 磯部祥子, 平川英樹, 久松完, 中野善公, 八木雅史, 大宮あけみ

    農研機構野菜花き研究部門成果情報(Web)   2020   2020

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  • Linkage map construction and de novo whole genome sequencing in Eustoma grandhiflorum

    白澤健太, 有本龍平, 石森元幸, 宮坂昌実, ゲルフィ アンドレア, 平川英樹, 遠藤誠, 河鰭実之, 磯部祥子

    育種学研究   22   2020   ISSN:1344-7629

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  • Construction of spinach pseudomolecules to enhance breeding efficiency

    平川英樹, 豊田敦, 伊藤武彦, 鈴木穣, 永野惇, 杉山優, 小野寺康之

    育種学研究   22   2020   ISSN:1344-7629

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  • Expression pattern analysis of candidate genes for dioecism and monoecism in spinach

    須藤有紀, 長部高之, 平川英樹, 鈴木穣, 小野寺康之

    育種学研究   22   2020   ISSN:1344-7629

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  • An exploration of genes related with abnormal stamen in cultivated strawberry with considering for the pedigree information

    永野聡一郎, 野口裕司, 平川英樹, 磯部祥子

    園芸学研究 別冊   19 ( 1 )   2020   ISSN:1881-8307

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  • Publication of the of ficial version of P1antGARDEN, a plant genome infomation portal site

    市原寿子, 原田大士朗, GHELFI A., 小原光代, 山田学, 白澤沙知子, FAWCETT J., 田村卓郎, 杉原英志, 中谷明弘, 中村保一, 平川英樹, 田畑哲之, 磯部祥子

    育種学研究   22   2020   ISSN:1344-7629

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  • 植物ゲノム情報ポータルサイトPlant GARDENの正規版公開

    市原寿子, 原田大士朗, ゲルフィ アンドレア, 小原光代, 山田学, 白澤沙知子, フォーセット ジェフリー, 田村卓郎, 杉原英志, 中谷明弘, 中村保一, 平川英樹, 田畑哲之, 磯部祥子

    日本分子生物学会年会プログラム・要旨集(Web)   43rd   2020

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  • 根粒菌共生効率を制御するマメ科植物プロテアーゼ

    下田宜司, 梅原洋佐, 伊藤(山谷)紘子, 林誠, 山崎俊正, 西ヶ谷有輝, 稲垣言要, 箱山雅生, 河内宏, 柴田哲, HOSSAIN Md Shakhawat, 佐藤修正, 平川英樹, 金子貴一, 川口正代司

    農研機構生物機能利用研究部門成果情報(Web)   2020   2020

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  • QTL analysis of important agronomic traits in spinach using pseudomolecules

    小野寺康之, 杉山優, 豊田敦, 伊藤武彦, 鈴木穣, 永野惇, 平川英樹

    育種学研究   22   2020   ISSN:1344-7629

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  • De novo whole-genome assembly in interspecific hybrid table grape, ‘Shine Muscat’

    白澤健太, 東暁史, 谷口郁也, 山本俊哉, 佐藤明彦, GELFI A., 平川英樹, 磯部祥子

    園芸学研究 別冊   19 ( 1 )   2020   ISSN:1881-8307

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  • 農耕地利用の強度に応答したアーバスキュラー菌根菌群集の収斂と多様性の維持機構

    丹羽理恵子, 佐藤修正, 佐藤修正, 平川英樹, 吉田重信, 佐藤孝, 鈴木貴恵, 佐藤匠, 俵谷圭太郎, 福永亜矢子, 小八重善裕, 大友量, 林正紀, 唐澤敏彦, 神山拓也, 丸山隼人, 江沢辰広

    日本土壌肥料学会講演要旨集(Web)   66   2020   ISSN:2424-0575

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  • 3-1-8 農耕地管理強度に沿ったアーバスキュラー菌根菌群集の入れ子構造:その生存戦略とインパクト(3-1 土壌生物の生態と機能,2019年静岡大会)

    丹羽 理恵子, 小八重 善裕, 大友 量, 林 正紀, 唐澤 敏彦, 神山 拓也, 丸山 隼人, 江沢 辰広, 佐藤 修正, 平川 英樹, 吉田 重信, 佐藤 孝, 鈴木 貴恵, 佐藤 匠, 俵谷 圭太郎, 福永 亜矢子

    日本土壌肥料学会講演要旨集   65 ( 0 )   24 - 24   2019   ISSN:0288-5840

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    Language:Japanese   Publisher:一般社団法人 日本土壌肥料学会  

    DOI: 10.20710/dohikouen.65.0_24_2

  • Comparative genomics to understand evolution of Alkaloid biosynthesis and diversification

    RAI Amit, NAKABAYASHI Ryo, HIRAKAWA Hideki, TSUGAWA Hiroshi, NAKAYA Taiki, MORI Tetsuya, TAKAHASHI Hiroki, KIKUCHI Shinji, SAITO Kazuki, SAITO Kazuki, YAMAZAKI Mami

    日本植物生理学会年会(Web)   60th   2019

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  • アジアのダイコン在来品種におけるFLC遺伝子の構造多型と抽苔早晩性との関連解析

    川端泉穂, 小林寛人, 白澤健太, 吹野伸子, 平川英樹, 北柴大泰

    育種学研究   21   2019   ISSN:1344-7629

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  • Hi-Cを用いたサブクローバゲノムのPseudomolecules構築

    磯部祥子, 白澤健太, GHELFI Andrea, MORAGA Roger, 平川英樹, 長崎英樹, GRIFFITHS Andrew, JACOBS Jeanne, GHAMKHAR Kioumars

    育種学研究   21   2019   ISSN:1344-7629

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  • イチゴ全ゲノム配列の更新とQTL-Seq解析への応用

    白澤健太, 和田卓也, 平田千春, 永松志朗, 森美幸, 田中幹大, 山本英司, 平川英樹, 磯部祥子

    育種学研究   21   2019   ISSN:1344-7629

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  • Utilization of root-knot nematode genome sequence information for identification of infection-related genes

    足立湧樹, 桑原大芽, 白澤健太, 平川英樹, 岩堀英晶, 浅水恵理香

    Nematological Research   49 ( 2 )   2019   ISSN:0919-6765

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  • サクラ「ソメイヨシノ」の全ゲノム配列の解読

    白澤健太, 江角智也, 平川英樹, 田中秀幸, 板井章浩, GHELFI Andrea, 長崎英樹, 磯部祥子

    園芸学研究 別冊   18 ( 1 )   2019   ISSN:1881-8307

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  • キク二倍体近縁野生種キクタニギクの全ゲノムの塩基配列の解読

    住友克彦, 平川英樹, 久松完, 永野聡一郎, 白澤健太, 樋口洋平, 草場信, 腰岡政二, 中野善公, 八木雅史, 山口博康, 谷口研至, 中野道治, 磯部祥子

    農研機構野菜花き研究部門成果情報(Web)   2019   2019

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  • カラマツにおける分子育種に向けたゲノムおよびバイオリソースの整備

    三嶋賢太郎, 平川英樹, 井城泰一, 田村明, 松下通成, 高島有哉, 永野聡一郎, 平尾知士, 福田陽子, 矢野慶介, 花岡創, 玉城聡, 武津英太郎, 栗田学, 平岡裕一郎, 生方正俊, 中田了五, 高橋誠

    日本森林学会大会学術講演集   130th   2019   ISSN:2187-6576

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  • イチジク株枯真性抵抗性を有するイヌビワの全ゲノム解読

    白澤健太, 薬師寺博, 森田剛成, 軸丸祥大, 池上秀利, 豊田敦, 平川英樹, 磯部祥子

    園芸学研究 別冊   18 ( 2 )   2019   ISSN:1881-8307

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  • ジオウの根肥大化に関わる遺伝子の探索-KIN2-like遺伝子の発現解析-

    河野徳昭, 桑原佑典, 乾貴幸, 平川英樹, 鈴木秀幸, 川原信夫, 吉松嘉代

    日本植物細胞分子生物学会大会・シンポジウム講演要旨集   37th   2019

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  • トランスクリプトーム解析によるニンニク遺伝資源のSNP情報の収集・整理

    佐藤修正, 平田翔, 平川英樹, 山田朋宏, 執行正義

    園芸学研究 別冊   18 ( 2 )   2019   ISSN:1881-8307

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  • ダイコン栽培品種および野生種におけるRsFLC1およびRsFLC2遺伝子の第一イントロンに存在する挿入多型の分布

    北柴大泰, 川端泉穂, 田阪初音, 白澤健太, 平川英樹, 吹野伸子

    育種学研究   21   2019   ISSN:1344-7629

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  • ダイコン品種「晩生桜島」の全ゲノム解析

    白澤健太, 平川英樹, 吹野伸子, 北柴大泰, 細川宗孝, 磯部祥子

    育種学研究   21   2019   ISSN:1344-7629

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  • ソバ属植物におけるゲノムの進化

    FAWCETT Jeffrey, FAWCETT Jeffrey, 上野まりこ, 大澤良, 大田竜也, 齊藤大樹, 齊藤大樹, 白澤健太, 竹島亮馬, 中崎鉄也, 西村和紗, 原尚資, 原尚資, 平川英樹, 松井勝弘, 水野信之, 安井康夫

    日本遺伝学会大会プログラム・予稿集   91st   2019

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  • ソバにおける異型花型自家不和合性遺伝子座のゲノム解析

    大田竜也, 相井城太郎, 上野まりこ, 大澤良, 齊藤大樹, 齊藤大樹, 白澤健太, 竹島亮馬, 中崎鉄也, 西村和紗, 原尚資, 原尚資, 平川英樹, FAWCETT J., FAWCETT J., 松井勝弘, 水野信之, 安井康夫

    育種学研究   21   2019   ISSN:1344-7629

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  • ホウレンソウY染色体雄特異的領域の座乗遺伝子同定および進化年代推定

    岡崎洋助, 平川英樹, 鈴木穣, 小野寺康之

    園芸学研究 別冊   18 ( 1 )   2019   ISSN:1881-8307

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  • 八倍体イチゴの大規模SNPタイピング

    磯部祥子, 白澤健太, 山本英司, 平川英樹, 七夕高也

    園芸学研究 別冊   18 ( 2 )   2019   ISSN:1881-8307

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  • ホウレンソウの性決定候補遺伝子の探索

    長部高之, 岩渕恵佑, 平川英樹, 鈴木穣, 小野寺康之, 小野寺康之

    育種学研究   21   2019   ISSN:1344-7629

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  • 圃場から単離したcheating根粒菌株のゲノム解析

    日下部翔平, 二反田正悟, 平川英樹, 中川知己, 中川知己, 佐藤修正

    植物微生物研究会研究交流会講演要旨集   29th   2019   ISSN:1341-0652

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  • 植物ゲノム統合ポータルサイトPlantGARDENの開発と公開

    原田大士朗, 市原寿子, 中谷明弘, ジェルフィ アンドレア, 山田学, 小原光代, 平川英樹, 田畑哲之, 磯部祥子

    日本植物細胞分子生物学会大会・シンポジウム講演要旨集   37th   2019

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  • 植物ゲノム情報ポータルサイトPlantGARDENの開発

    原田大士朗, 市原寿子, 中谷明弘, GHELFI A., 藤代継一, 小原光代, 平川英樹, 田畑哲之, 磯部祥子

    育種学研究   21   2019   ISSN:1344-7629

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  • 植物ゲノム情報ポータルサイトPlantGARDENの拡張

    原田大士朗, 市原寿子, 中谷明弘, GHELFI A., 山田学, 小原光代, 平川英樹, 田畑哲之, 磯部祥子

    育種学研究   21   2019   ISSN:1344-7629

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  • 栽培イチゴ雄蕊形態異常系統に特異的なゲノム配列の抽出

    永野聡一郎, 野口裕司, 平川英樹, 磯部祥子

    園芸学研究 別冊   18 ( 1 )   2019   ISSN:1881-8307

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  • 未利用地から農地への土地利用変化に伴う土壌微生物群集構造の変化

    高田理江, 花野滋, 花野滋, 宮本託志, 滝澤理仁, 冨永達, 柴田大輔, 柴田大輔, 櫻井望, 櫻井望, 平川英樹, 小林優

    日本土壌肥料学会講演要旨集(Web)   65   2019   ISSN:2424-0575

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  • 菌根菌叢・細菌叢同定ウェブインターフェースの開発

    平川英樹, 丹羽理恵子, 佐藤修正, 江沢辰広

    日本植物細胞分子生物学会大会・シンポジウム講演要旨集   37th   2019

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  • 雄花着花量の異なるスギクローンのジベレリン処理後の遺伝子発現解析

    坪村美代子, 三嶋賢太郎, 平尾知士, 永野聡一郎, 平川英樹

    日本森林学会大会学術講演集   130th   2019   ISSN:2187-6576

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  • 野生種および栽培種のイチゴ根圏における微生物叢の比較解析

    吉本達也, AKYOL Turgut Yigit, 佐藤修正, 平川英樹, 浅水恵理香

    植物微生物研究会研究交流会講演要旨集   29th   2019   ISSN:1341-0652

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  • 酢酸菌の呼吸鎖NADH脱水素酵素の進化と表現型に関する考察

    松谷峰之介, 平川秀樹, HEPPY Sriherfyna Feronika, 薬師寿治, 薬師寿治, 松下一信, 松下一信

    日本ゲノム微生物学会年会要旨集   13th   2019

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  • 連続塩基組成に基づく植物ゲノムにおける微生物由来水平伝播候補遺伝子の網羅的検出

    藤田由剛, 平川英樹, 池村淑道, 阿部貴志

    日本ゲノム微生物学会年会要旨集   13th   2019

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  • 農耕地管理強度に沿ったアーバスキュラー菌根菌群集の入れ子構造:その生存戦略とインパクト

    丹羽理恵子, 佐藤修正, 佐藤修正, 平川英樹, 吉田重信, 佐藤孝, 鈴木貴恵, 佐藤匠, 俵谷圭太郎, 福永亜矢子, 小八重善裕, 大友量, 林正紀, 唐澤敏彦, 神山拓也, 丸山隼人, 江沢辰広

    日本土壌肥料学会講演要旨集(Web)   65   2019   ISSN:2424-0575

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  • Allium cepaにおける全ゲノム解読に向けた取り組みについて

    執行正義, MOSTAFA Abdelrahman, MOSTAFA Abdelrahman, 佐藤修正, 平川英樹, 辻村真衣, 寺地徹, 豊田敦

    園芸学研究 別冊   17 ( 1 )   2018   ISSN:1881-8307

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  • アジア在来品種を主としたダイコンにおけるゲノムワイドなSNPsと遺伝的多様性

    小林寛人, 白澤健太, 吹野伸子, 平川英樹, 北柴大泰

    育種学研究   20   2018   ISSN:1344-7629

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  • カキ属の全ゲノム情報が明らかにする性の多様性を駆動した古倍化

    赤木剛士, 赤木剛士, 白澤健太, 長崎英樹, 平川英樹, 田尾龍太郎, COMAI Luca, HENRY Isabelle M.

    園芸学研究 別冊   17 ( 1 )   2018   ISSN:1881-8307

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  • サツマイモネコブセンチュウSPレースの遺伝子型解析

    浅水恵理香, 白澤健太, 平川英樹, 岩堀英晶

    Nematological Research   48 ( 2 )   2018   ISSN:0919-6765

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  • キク属モデル植物・キクタニギク(Chrysanthemum seticuspe)の全ゲノム解析

    平川英樹, 住友克彦, 久松完, 永野聡一郎, 永野聡一郎, 白澤健太, 樋口洋平, 草場信, 腰岡政二, 中野善公, 八木雅史, 山口博康, 谷口研至, 中野道治, 磯部祥子

    育種学研究   20   2018   ISSN:1344-7629

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  • キクタニギクの全ゲノムシーケンスを利用した花成関連遺伝子の網羅的探索

    樋口洋平, 久松完, 中野善公, 平川英樹, 白澤健太, 磯部祥子, 住友克彦

    園芸学研究 別冊   17 ( 2 )   2018   ISSN:1881-8307

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  • カーネーションの開花期に関するQTL解析

    八木雅史, 白澤健太, 平川英樹, 磯部祥子, 松野純子, 棚瀬幸司, 小野崎隆, 山口博康

    園芸学研究 別冊   17 ( 2 )   2018   ISSN:1881-8307

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  • ジオウの根肥大化に関わる遺伝子の探索(3)

    河野徳昭, 桑原佑典, 乾貴幸, 平川英樹, 平川英樹, 鈴木秀幸, 川原信夫, 吉松嘉代

    日本薬学会年会要旨集(CD-ROM)   138th   2018

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  • ダイコン遺伝資源の黒斑細菌病抵抗性評価

    吹野伸子, 北柴大泰, 平川英樹, 白澤健太, 板橋悦子, 柿崎智博, 小原隆由

    園芸学研究 別冊   17 ( 2 )   2018   ISSN:1881-8307

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  • ホウレンソウの性染色体における組換え抑制領域の進化年代の推定

    岡崎洋助, 平川英樹, 鈴木穣, 小野寺康之

    育種学研究   20   2018   ISSN:1344-7629

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  • 全ゲノム情報をベースとしたロゼット形成時におけるキクタニギクの遺伝子発現プロファイリング

    久松完, 住友克彦, 樋口洋平, 腰岡政二, 永野聡一郎, 永野聡一郎, 平川英樹, 磯部祥子

    園芸学研究 別冊   17 ( 2 )   2018   ISSN:1881-8307

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  • 全ゲノムシーケンスを活用したキクタニギク連鎖地図の作成および栽培ギクにおけるDNAマーカー開発

    白澤健太, 住友克彦, 平川英樹, 磯部祥子, 八木雅史, 中野善公, 久松完, 大宮あけみ, 中野道治, 谷口研至, 草場信

    園芸学研究 別冊   17 ( 2 )   2018   ISSN:1881-8307

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  • メタボロームリポジトリの設計と機能

    有田正規, 金谷重彦, 櫻井望, 平川英樹, 福島敦史

    日本分子生物学会年会プログラム・要旨集(Web)   41st   2018

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  • ミヤコグサが土壌微生物叢を操る仕組み

    中川知己, 中川知己, 佐伯和彦, 豊岡公徳, 佐藤繭子, 平川英樹, 大澤美芙, 若崎眞由美, 福原舞, 福原舞, 川東拓司, 吉田彩恵, 菅沼教生, 三井久幸, 佐藤修正, 川口正代司, 川口正代司

    日本植物生理学会年会(Web)   59th   2018

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  • ホウレンソウの雄決定遺伝子座周辺から見出された組換抑制領域の分子構造

    小野寺康之, 工藤友裕, 高橋光彦, 長部高之, 豊田敦, 平川英樹, 鈴木穣, 近江戸伸子

    園芸学研究 別冊   17 ( 1 )   2018   ISSN:1881-8307

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  • Systems biology approach to elucidate camptothecin biosynthesis pathways in-planta

    RAI Amit, HIRAKAWA Hideki, NAKABAYASHI Ryo, TSUGAWA Hiroshi, NAKAYA Taiki, MORI Tetsuya, SUZUKI Hieyuki, TAKAHASHI Hiroki, SAITO Kazuki, SAITO Kazuki, YAMAZAKI Mami

    日本植物細胞分子生物学会大会・シンポジウム講演要旨集   36th   2018

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  • 機械学習アルゴリズムを用いたネギにおけるアーバスキュラー菌根菌接種効果の発現予測

    丹羽理恵子, 佐藤修正, 佐藤修正, 平川英樹, 吉田重信, 佐藤孝, 鈴木貴恵, 齋藤雅典, 齋藤雅典, 佐藤匠, 俵谷圭太郎, 福永亜矢子, 江沢辰広

    日本土壌肥料学会講演要旨集   64   2018   ISSN:0288-5840

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  • 植物ゲノム情報ポータルサイト・PlantGARDENの開発にむけて

    原田大士朗, 市原寿子, 中谷明弘, GHELFI Andrea, 藤代継一, 小原光代, 平川英樹, 田畑哲之, 磯部祥子

    日本分子生物学会年会プログラム・要旨集(Web)   41st   2018

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  • 植物ゲノム情報ポータルサイト・PlantGARDENの開発と植物ゲノム解析の現状

    原田大士朗, 市原寿子, 中谷明弘, GHELFI A., 藤代継一, 小原光代, 平川英樹, 田畑哲之, 磯部祥子

    育種学研究   20   2018   ISSN:1344-7629

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  • 現地農家圃場等におけるネギへのAM菌資材の接種効果

    鈴木貴恵, 丹羽理恵子, 丹羽理恵子, 宇野亨, 田島亮介, 伊藤豊彰, 伊藤豊彰, 佐藤修正, 平川英樹, 吉田重信, 江沢辰広, 齋藤雅典, 齋藤雅典

    日本土壌肥料学会講演要旨集   64   2018   ISSN:0288-5840

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  • 雄蕊形態異常を伴う栽培イチゴ核置換系統間のゲノム変異の検出

    永野聡一郎, 永野聡一郎, 野口裕司, 平川英樹, 磯部祥子

    園芸学研究 別冊   17 ( 1 )   2018   ISSN:1881-8307

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  • 酢酸菌における膜結合型NADH脱水素酵素の分布について

    松谷峰之介, 平川英樹, SRIHERFYNA Feronika Heppy, 片岡尚也, 片岡尚也, 薬師寿治, 薬師寿治, 松下一信, 松下一信

    日本分子生物学会年会プログラム・要旨集(Web)   41st   2018

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  • 菌根菌叢および細菌叢のウェブ上解析インターフェースの開発

    平川英樹, 丹羽理恵子, 佐藤修正, 江沢辰広

    日本ゲノム微生物学会年会要旨集   12th   2018

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  • dd-RAD-Seq法によるアブラナ科作物の多型解析

    磯部祥子, 白澤健太, 平川英樹

    育種学研究   19   2017   ISSN:1344-7629

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  • アーバスキュラー菌根菌接種の残効が翌年のダイズ生育へ及ぼす影響

    神山拓也, 丹羽理恵子, 安達克樹, 江沢辰広, 鈴木崇之, 佐藤修正, 佐藤修正, 平川英樹, 吉田重信

    日本作物学会講演会要旨集   243rd   2017

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  • RAD-seq法を用いたキクタニギク細葉原因遺伝子NEEDLE LEAF1のマッピング

    中野道治, 有賀悠貴, 小塚俊明, 平川英樹, 住友克彦, 八木雅史, 中野善公, 久松完, 磯部祥子, 谷口研至, 草場信

    園芸学研究 別冊   16 ( 2 )   2017   ISSN:1881-8307

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  • RAD-Seqを用いたアジサイ’城ヶ崎’由来の八重咲き性因子と連鎖するSNPsの探索

    奈島賢児, 白澤健太, 平川英樹, 磯部祥子, 巣山拓郎, 下村克己, 平島敬太, 和田卓也, 黒倉健, 阿久津翠, 小玉雅晴, 小玉雅晴, 生井潔

    園芸学研究 別冊   16 ( 2 )   2017   ISSN:1881-8307

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  • Plant Genome Database Japan(PGDBj)におけるDNAマーカーとQTL情報の公開

    柴谷多恵子, 市原寿子, 田村卓郎, 白澤沙知子, 浅水恵理香, 平川英樹, 田畑哲之

    育種学研究   19   2017   ISSN:1344-7629

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  • PGDBjにおけるQTLおよびDNAマーカー検索インターフェースの改良と近年の研究動向

    柴谷多恵子, 市原寿子, 白澤沙知子, 浅水恵理香, 平川英樹, 田畑哲之

    園芸学研究 別冊   16 ( 1 )   2017   ISSN:1881-8307

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  • De novo transcriptome解析によるトウサイカチサポニン合成経路に関わる遺伝子群の探索

    桑原佑典, 中島大輔, 新保さやか, 中村道美, 河野徳昭, 川原信夫, 山崎真巳, 齊藤和季, 鈴木秀幸, 平川英樹, 平川英樹

    日本生薬学会年会講演要旨集   64th   2017   ISSN:0919-1992

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  • イチゴの果実硬度に関するゲノミックセレクションの試み

    永野聡一郎, 白澤健太, 平川英樹, 前田ふみ, 渡邉学, 野口裕司, 片岡園, 坪根正雄, 奥幸一郎, 田崎公久, 飯村一成, 中谷明弘, 柳智博, 磯部祥子

    園芸学研究 別冊   16 ( 2 )   2017   ISSN:1881-8307

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  • サツマイモネコブセンチュウ系統のゲノム多型解析

    浅水恵理香, 白澤健太, 平川英樹, 岩堀英晶

    植物微生物研究会研究交流会講演要旨集   27th   2017   ISSN:1341-0652

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  • サツマイモ2倍体野生種および6倍体栽培種の全ゲノム解析

    長崎英樹, YOON Yng-Han, CAO Qinghe, 白澤健太, LIU Qingchang, JEONG Jae Cheol, 田中勝, 平川英樹, ZHAI Hong, 岡田吉弘, HAHN Jang-Ho, KWAK Sang-Soo, MA Dai-Fu, 磯部祥子

    育種学研究   19   2017   ISSN:1344-7629

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  • キク属におけるモデル系統の開発とマップベースクローニングの試み

    有賀悠貴, 中野道治, 小塚俊明, 増田優, 平川英樹, 住友克彦, 八木雅史, 中野善公, 久松完, 磯部祥子, 谷口研至, 草場信

    育種学研究   19   2017   ISSN:1344-7629

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  • キクタニギクのゲノム配列解読

    平川英樹, 住友克彦, 久松完, 中野善公, 八木雅史, 中野道治, 白澤健太, 草場信, 磯部祥子

    園芸学研究 別冊   16 ( 1 )   2017   ISSN:1881-8307

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  • カキ属の全ゲノム配列解読(第1報):系統特異的なゲノム進化

    赤木剛士, 赤木剛士, 白澤健太, 長崎英樹, 平川英樹, COMAI Luca, 田尾龍太郎, HENRY Isabelle M.

    園芸学研究 別冊   16 ( 2 )   2017   ISSN:1881-8307

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  • オウトウゲノムの概要配列の決定

    白澤健太, 五十鈴川寛司, 池永充伸, 齋藤裕太郎, 齋藤裕太郎, 山本俊哉, 平川英樹, 磯部祥子

    園芸学研究 別冊   16 ( 2 )   2017   ISSN:1881-8307

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  • イチゴ属の異質倍数化とゲノム構造の多様化に伴う形質および生育地環境の多様化

    永野聡一郎, 白澤健太, 平川英樹, 林篤司, 七夕高也, 磯部祥子

    日本生態学会大会講演要旨(Web)   64th   2017

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  • ジオウの根肥大化に関わる遺伝子の探索(2)

    河野徳昭, 桑原佑典, 乾貴幸, 平川英樹, 平川英樹, 鈴木秀幸, 川原信夫, 吉松嘉代

    日本植物細胞分子生物学会大会・シンポジウム講演要旨集   35th   2017

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  • ホースグラムのドラフトゲノム解析

    平川英樹, RAKESH C., 白澤健太, 永野聡一郎, 長崎英樹, TILAK S., 磯部祥子

    育種学研究   19   2017   ISSN:1344-7629

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  • 四倍体ニラにおける複相大胞子形成性連鎖マーカーの作出

    若桝睦子, 田口久美子, 中澤佳子, 田崎公久, 平川英樹, 磯部祥子, 飯村一成, 天谷正行, 松本紀子, 大島一則, 生井潔

    育種学研究   19   2017   ISSN:1344-7629

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  • 同質六倍体サツマイモ栽培種のゲノム解読に向けた取り組み

    白澤健太, 長崎英樹, 田中勝, 岡田吉弘, 高畑康浩, 平川英樹, 磯部祥子

    日本植物学会大会研究発表記録   81st   2017

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  • ミヤコグサはいかにして働かないcheating根粒菌を排除するのか?

    中川知己, 中川知己, 佐伯和彦, 豊岡公徳, 佐藤繭子, 平川英樹, 大澤美芙, 若崎眞由美, 福原舞, 福原舞, 川東拓司, 吉田彩恵, 菅沼教生, 佐藤修正, 三井久幸, 岡崎伸, 川口正代司, 川口正代司

    植物微生物研究会研究交流会講演要旨集   27th   2017   ISSN:1341-0652

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  • 栽培イチゴ(Fragaria×ananassa)MAGIC集団を用いた完着期果実の遺伝子発現プロファイリング

    永野聡一郎, 平川英樹, 和田卓也, 田崎公久, 前田ふみ, GHELFI Andrea, 森美幸, 鶴見理沙, 津金胤昭, 坪根正雄, 飯村一成, 白澤健太, 奥幸一郎, 大橋隆, 渡邉学, 生井潔, 磯部祥子

    園芸学研究 別冊   16 ( 2 )   2017   ISSN:1881-8307

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  • 植物ゲノム統合データベースPGDBjの新しいツールの紹介

    市原寿子, 柴谷多恵子, 田村卓郎, 白澤沙知子, 中谷明弘, 浅水恵理香, 中村保一, 平川英樹, 田畑哲之

    育種学研究   19   2017   ISSN:1344-7629

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  • 植物ゲノムからの微生物由来水平伝播候補遺伝子の網羅的な検出

    藤田由剛, 平川英樹, 阿部貴志

    日本生化学会大会(Web)   90th   2017

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  • 栽培バラの祖先種であるノイバラ(Rosa multiflora)のドラフトゲノム

    中村典子, 平川英樹, 佐藤修正, 太田垣駿吾, 松本省吾, 田畑哲之, 田中良和

    日本植物細胞分子生物学会大会・シンポジウム講演要旨集   35th   2017

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  • 異質八倍体栽培イチゴゲノムのフェージング配列の染色体への位置付けと祖先ゲノムの推定

    白澤健太, 平川英樹, 寺地真由子, 永野聡一郎, 長崎英樹, 前田ふみ, 柳智博, 磯部祥子

    育種学研究   19   2017   ISSN:1344-7629

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  • 管理・環境要因に基づいたネギにおけるアーバスキュラー菌根菌接種効果発現の予測モデル構築

    丹羽理恵子, 佐藤修正, 佐藤修正, 平川英樹, 吉田重信, 佐藤孝, 鈴木貴恵, 齋藤雅典, 佐藤匠, 俵谷圭太郎, 福永亜矢子, 江沢辰広

    日本土壌肥料学会講演要旨集   63   2017   ISSN:0288-5840

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  • サツマイモ2倍体野生種Ipomoea trifidaの全ゲノム解析

    YOON Ung‐Han, 長崎秀樹, 田中勝, 平川英樹, 白澤健太, 永野聡一郎, 岡田吉弘, 田淵宏朗, 高畑康浩, HAHN Jang‐Ho, 磯部祥子

    育種学研究   18   67   2016.3   ISSN:1344-7629

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    Language:Japanese  

    DOI: 10.1270/jsbbr.18.67

    J-GLOBAL

  • Allium cepaにおける超高密度連鎖地図作成の試み

    山北和香, 竹富詩歩, 佐藤修正, 平田翔, 平川英樹, 田中啓介, 峯洋子, 山内直樹, 執行正義

    園芸学研究 別冊   15 ( 1 )   2016   ISSN:1881-8307

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  • RNA-seqおよび濃縮ライブラリーによるニラSSRマーカーの大量開発

    田崎公久, 若桝睦子, 生井潔, 平川英樹, 笹本茂美, 寉岡久乃, 南千春, 磯部祥子

    DNA多型   24 ( 1 )   2016   ISSN:2188-3815

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  • RAD-Seq法を用いたオウトウの高密度統合連鎖地図の開発とバラ科果樹ゲノムとの比較解析

    白澤健太, 五十鈴川寛司, 池永充伸, 齋藤裕太郎, 平川英樹, 磯部祥子

    園芸学研究 別冊   15 ( 2 )   2016   ISSN:1881-8307

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  • PGDBjより新たに公開した「育種向けDNAマーカー検索ページ」について

    柴谷多恵子, 白澤沙知子, 市原寿子, 浅水恵理香, 平川英樹, 田畑哲之

    園芸学研究 別冊   15 ( 2 )   2016   ISSN:1881-8307

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  • DenovoMAGICによるイチゴの全ゲノム解析

    平川英樹, 白澤健太, 長崎英樹, 永野聡一郎, 前田ふみ, 磯部祥子

    育種学研究   18   2016   ISSN:1344-7629

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  • アーバスキュラー菌根菌接種資材の作物根への定着に関わる生態的要因

    丹羽理恵子, 丸山隼人, 佐藤修正, 平川英樹, 吉田重信, 大友量, 小八重善裕, 佐藤孝, 唐澤敏彦, 林正紀, 福永亜矢子, 安達克樹, 神山拓也, 江沢辰広

    日本土壌微生物学会講演要旨集   2016   2016

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  • ゲノム情報を用いたアプローチによる酢酸菌Komagataeibacter属の分類学的位置付けの検証

    新村梨恵, 松谷峰之介, 石川森夫, 矢吹岳, 海野祥子, 志波優, 鈴木治夫, 平川英樹, 吉川博文, 吉川博文, 松下一信, 小泉幸道, 貝沼(岡本)章子

    日本農芸化学会大会講演要旨集(Web)   2016   2016   ISSN:2186-7976

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  • イチゴのハプロタイプ同定に向けた全ゲノム解析

    永野聡一郎, 白澤健太, 長崎英樹, 平川英樹, 前田ふみ, 磯部祥子

    園芸学研究 別冊   15 ( 2 )   2016   ISSN:1881-8307

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  • サブクローバの全ゲノム解析

    平川英樹, KAUR Parwinder, 白澤健太, NICHOLS Phillip, 永野聡一郎, APPELS Rudi, ERSKINE William, 磯部祥子

    日本草地学会誌   62   2016   ISSN:0447-5933

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  • ネギ属トランスクリプトームデータベースAllium TDBを活用したAllium cepa連鎖地図の構築

    藤戸聡史, 山下謙一郎, 山下謙一郎, 若生忠幸, 塚崎光, 塚崎光, 山北和香, 佐藤修正, 平川英樹, 執行正義

    園芸学研究 別冊   15 ( 2 )   2016   ISSN:1881-8307

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  • ネギにおけるアーバスキュラー菌根菌接種菌と土着菌との競合および接種効果発現に関わる環境要因

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    日本土壌肥料学会講演要旨集   62   2016   ISSN:0288-5840

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  • ターゲットアンプリコンシークエンス法による高オレイン酸ラッカセイ育種系統のゲノムワイドSNP遺伝子型の決定

    白澤健太, 桑田主税, 渡邉学, 深見正信, 平川英樹, 磯部祥子

    育種学研究   18   2016   ISSN:1344-7629

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  • ソバのゲノム解読と突然変異育種への応用

    安井康夫, 上野まりこ, 平川英樹

    イオンビーム育種研究会大会講演要旨集   11th   2016

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  • ホウレンソウ性染色体とテンサイ常染色体の比較解析

    高畠聡史, 岩渕恵佑, 平川英樹, 小野寺康之

    育種学研究   18   2016   ISSN:1344-7629

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  • 同質六倍体で2n=6x=90のゲノムを持つサツマイモ栽培種の高密度SNP遺伝地図の作成

    白澤健太, 田中勝, 高畑康浩, MA Daifu, CAO Qinghe, LIU Qingchang, ZHAI Hong, KWAK Sang Soo, JEONG Jae Cheol, YOON Ung Han, 平川英樹, 磯部祥子

    育種学研究   18   2016   ISSN:1344-7629

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  • 植物ゲノム関連情報を統合するためのポータルサイトPGDBjのコンテンツに対するセマンティックウェブ技術の適用

    市原寿子, 白澤沙知子, 柴谷多恵子, 中谷明弘, 中村保一, 浅水恵理香, 平川英樹, 田畑哲之

    育種学研究   18   2016   ISSN:1344-7629

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  • 酢酸菌Acetobacter pasteurianus12株のゲノム情報と耐熱性との相関に関する解析

    松谷峰之介, 山下隆司, 古川藍子, 辰野真木, 貝沼(岡本)章子, 石川森夫, 志波優, 吉川博文, 吉川博文, 平川英樹, 薬師寿治, 松下一信

    日本ゲノム微生物学会年会要旨集   10th   2016

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  • Aminobacter属に属するミヤコグサ根粒菌のゲノム解析

    眞板寛子, 王明卓, 窪田和奈, 平川英樹, 平川英樹, 佐伯和彦, 佐藤修正

    日本ゲノム微生物学会年会要旨集   9th   2015

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  • Axiomジェノタイピングアレイを用いた栽培イチゴの超高密度SNP連鎖地図の作成

    永野聡一郎, 白澤健太, 平川英樹, 前田ふみ, 石川正美, 磯部祥子

    園芸学研究 別冊   14 ( 2 )   2015   ISSN:1881-8307

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  • イチゴ果実のアントシアニン合成に関わる遺伝子発現解析

    平川英樹, 田崎公久, 生井潔, 大橋隆, 前田ふみ, 渡邊学, 和田卓也, 平島敬太, 下村克己, 白澤健太, 磯部祥子

    育種学研究   17   2015   ISSN:1344-7629

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  • カーネーション標準連鎖地図を利用した八重咲きに連鎖したSSRマーカーの開発

    八木雅史, 山本俊哉, 磯部祥子, 平川英樹, 田畑哲之, 棚瀬幸司, 山口博康, 小野崎隆

    花き研究所成果情報(Web)   2015   2015

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  • ソルガム,トランスクリプトームデータベースの更新

    蒔田由布子, 嶋田勢津子, 川島美香, 栗山朋子, 平川英樹, 佐藤修正, 松井南

    日本植物細胞分子生物学会大会・シンポジウム講演要旨集   33rd   2015

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  • ネギ属バイオリーソースを用いたトランスクリプトーム解析データの活用

    執行正義, 佐藤修正, ABDELRAHMAN Mostafa, 平田翔, 平川英樹, 田中啓介, 峯洋子, 杉山信男, 山内直樹

    園芸学研究 別冊   14 ( 2 )   2015   ISSN:1881-8307

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  • ネギ単一異種染色体添加系統のRNA-Sequencingによるシャロット染色体マーカーの大量取得

    山北和香, 佐藤修正, ABDELRAHMAN Mostafa, 平田翔, 平川英樹, 田中啓介, 峯洋子, 山内直樹, 執行正義

    園芸学研究 別冊   14 ( 2 )   2015   ISSN:1881-8307

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  • ネギの発現遺伝子配列を活用したDNAマーカー

    塚崎光, 谷口成紀, 佐藤修正, 平川英樹, 片寄裕一, 金森裕之, 伊藤剛, 福岡浩之, 山下謙一郎, 執行正義, 若生忠幸

    農研機構野菜茶業研究所成果情報(Web)   2015   2015

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  • トランスクリプトーム情報を利用したホウレンソウ性連鎖遺伝子群の網羅的同定

    高畠聡史, 平川英樹, 鈴木穣, 小野寺康之

    育種学研究   17   2015   ISSN:1344-7629

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  • トマトの高品質多収育種のためのゲノム情報に基づく高精度形質予測

    山本英司, 松永啓, 小野木章雄, 鐘ケ江弘美, 南川舞, 鈴木晶統, 白澤健太, 平川英樹, 布目司, 山口博隆, 宮武宏治, 大山暁男, 岩田洋佳, 福岡浩之

    農研機構野菜茶業研究所成果情報(Web)   2015   2015

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  • トマトの新規変異体pale yellow petal 2の生化学的研究

    竹澤里実, 岸本早苗, 平川英樹, 白澤健太, 大宮あけみ, 江面浩, 有泉亨

    日本植物細胞分子生物学会大会・シンポジウム講演要旨集   33rd   2015

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  • トマトにおけるRAD-Seq法の効率的な利用法の検討と高密度連鎖地図の作成

    白澤健太, 平川英樹, 磯部祥子

    園芸学研究 別冊   14 ( 2 )   2015   ISSN:1881-8307

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  • ミヤコグサ根粒菌のNaCl耐性に関する比較ゲノムおよび分子遺伝学解析

    窪田和奈, 大澤美芙, 眞板寛子, 眞板寛子, 平川英樹, 佐藤修正, 佐伯和彦

    日本生化学会大会(Web)   88th   2015

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  • ミヤコグサ根粒菌野生系統を用いた耐塩性関連遺伝子の探索

    窪田和奈, 大澤美芙, 眞板寛子, 眞板寛子, 平川英樹, 佐藤修正, 佐伯和彦

    植物微生物研究会研究交流会講演要旨集   25th   2015   ISSN:1341-0652

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  • 日和見病原菌Asaia bogorensisの環境適応遺伝子群

    河合幹彦, 河合幹彦, 東裏典枝, 東裏典枝, 早崎君江, 平川英樹, 武部聡, 松下一信, 東慶直

    日本ゲノム微生物学会年会要旨集   9th   2015

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  • 様々な倍数性や接合性のゲノムを持つ作物種におけるRAD-seq法の利用

    白澤健太, 平川英樹, 磯部祥子