||Clock and sleep in a cnidarian, Hydra..
||MIYOKAWA, R., TSUDA, T., KANAYA, H. J., KUSUMI, J., TACHIDA, H., AND KOBAYAKAWA, Y., Horizontal transmission of Chlorococcum causes morphological and gene expression changes in Hydra vulgaris 105 strain, International Workshop "At the roots of bilaterian complexity: insights from early emerging metazoans", 2019.09.
||Mitsuhiro Aizu, Shin Nishida, Junko Kusumi, Yuko Tajima, Masao Amano, Motoi Yoshioka, Tadasu K. Yamada, Kunio Araya, Genetic variation of MHC genes in the Japanese finless porpoise (Neophocaena asiaeorientalis sunameri) , The 21th Biennial Conference on the Biology of Marine Mammals, 2015.12, Finless porpoise, Neophocaena asiaeorientalis sunameri, is distributed from the Taiwan Strait to Japanese waters. It inhibits in shallow waters close to shore and has been under considerable human impacts through habitat destruction and/or bycatch, and recent decline of the population size was reported in Japanese waters. In parallel to measuring the levels of genetic diversity in neutral markers, we also investigated a functional genetic marker under selection, the major histocompatibility complex (MHC), to obtain the information of demographics and adaptation processes within/among populations in Japan. MHC plays a key role in the initiation of immune response, and it is one of the most important genetic systems for infectious disease resistance in vertebrates. The decline of population size will lead the loss of diversity of MHC genes, ultimately reducing the ability of immune function to suppress an infection. Therefore, the assessment of MHC genes is greatly important in conservation genetics. Here, we analyzed two loci of MHC genes, DRB locus for 102 individuals and DQB locus for 88 individuals from five populations in Japanese waters. We found that there were totally six alleles at MHC DRB locus of which frequencies differed among local populations. Eight alleles were found in DQB locus and one of them was reported from Chinese waters. DRB locus had lower heterozygosity (HO=0.11) compared to DQB locus (HO=0.68). The patterns of population differentiation of each MHC locus were not identical and were differed from one of the microsatellite loci, a neutral genetic marker. Both loci showed a sign of positive selection (dN/dS>1). These results suggest that regional adaptations on each MHC locus, which correspond to different selection pressures from different pathogens, occurred among Japanese populations. .
||Yuka Ikezaki, Yoshihisa Suyama, Beth A. Middleton, Yoshihiko Tsumura, Junko Kusumi, Kosuke Teshima, Hidenori Tachida, Inference of population structure in Taxodium distichum, a coniferous tree in North America, based on amplicon sequence analysis, SMBE Satellite Meeting / NIG International Symposium: The Causes of Genome Evolution, 2014.03, Taxodium distichum is a long-lived coniferous tree widely distributed in southeast North America. It prefers wetlands and has two varieties, bald-cypress and pond-cypress in the United States. These two varieties have clearly different habitats and morphological characteristics. From the results of previous studies, both geographical (between the Florida and Mississippi River regions) and variety specific differentiations were suggested (Tsumura et al., 1999; Lickey and Walker, 2002; Kusumi et al., 2010; Tanaka et al., 2012). The distributions of the two varieties overlapped in the Florida and southern Mississippi River regions, hence the geographical and variety specific differentiations are related in a complex way. Recently, the Next Generation Sequencing (NGS) approach along with amplicon sequence analyses enables us to obtain sequences of many individuals at many loci fairly easily. To infer the detail of population structure of Taxodium, we collected 96 individuals from the two varieties in the Mississippi River, Texas and Florida regions and determined their sequences at 48 nuclear loci using this approach with a GS FLX 454 sequencer. To examine the level of differentiation at neutral loci, we randomly selected genes from an annotated Expressed Sequence Tag (EST) library of Taxodium. The results of a Bayesian clustering analysis and estimated FST values suggested that the populations in the Mississippi River and Texas regions had similar genetic constitution and they are differentiated from the populations in the Florida region though the level of the differentiation was low. The variety specific differentiation was also found, however it was attributed to five loci showing much higher FST values than the other loci. After removing these loci, the Bayesian clustering analysis showed only geographical differentiation. Finally, analyses of the geographical and variety subdivisions assuming the isolation with migration model suggested that the divergence time of the variety subdivision was much older than that of the geographical subdivision (4.6 MYA and 0.2 MYA, respectively). However, a high level of migration from the bald-cypress populations to the pond-cypress populations (2Nu = 10.0) has reduced the level of the variety specific differentiation. On the other hand, the level of migration between the Mississippi-Texas region and Florida region was low (from Mississippi-Texas populations to Florida populations: 0.28; from Florida populations to Mississippi-Texas populations: 0.30), so the level of geographical differentiation seemed to have been increasing. .
||Junko Kusumi, Motoshi Ichinose, Masasuke Takefu, Wolfgang Stephan, Masaru Iizuka, A model of compensatory molecular evolution with indirect compensation, SMBE Satellite Meeting / NIG International Symposium: The Causes of Genome Evolution, 2014.03, If there is an extra pair of sites that can reduce the deleterious effects of single mutants at directly interacted pair of sites, this reduction is called indirect compensation. This idea was motivated by compensatory molecular evolution of t-RNA secondary structure.  A previous study reported that a mutation that destroyed a Watson-Crick pair in a t-RNA stem structure could be compensated by creation of a new pair in the neighborhood. This phenomenon appears in molecular evolution of t-RNAs in mammalian lineages repeatedly. This observation indicates that compensatory evolution could occur not only by a mutation at directly interacted pair of sites but also a mutation at extra sites neighboring the original pair sites by forming a new bond. Here, we considered the effects of “indirect compensation” on the rate of compensatory molecular evolution by introducing a simple mathematical model. Computer simulations demonstrate that the effect of indirect compensation effectively decrease the fixation time of double mutants of direct compensatory sites if mutation is weak (4Nu = 0.01, 0.1) and deleterious effect of selection is strong (4Ns > 3). The degree of reduction of the fixation time depends on the relative ratio of mutation rate to selection intensity. Further, we investigate properties of sample paths by classifying them to, direct pathway, indirect pathway I and indirect pathway II. Each pathway corresponds to no change on indirect compensatory site, the first change on direct compensatory sites and the second change on indirect compensatory site, and the first change on indirect compensatory site and the second change on direct compensatory sites. It is shown that most of the double mutants appear through the indirect pathway II when selection is strong. This pathway enables individuals to complete compensatory molecular evolution without reducing fitness if a mutation at indirect compensation site compensates completely the deleterious effects of single mutants at directly interacted pair of sites. Our results suggest that the compensatory evolution with indirect compensation may be responsible to the molecular evolution of t-RNA secondary structure. .
||Mitsuhiro Aizu, Junko Kusumi, Shin Nishida, Yuko Tajima, Tadasu K. Yamada, Masao Amano, Kunio Araya, Genetic Population Structure of Finless Porpoise in Japanese Coastal Waters, International Whaling Comission, 2013.06, To clarify fine-scale population genetic structure, levels of genetic diversity, and population history of the finless porpoise, Neophocaena phocaenoides, in Japanese waters, we analysed 10 microsatellite (MS-DNA) loci and mtDNA control region sequence (853bp) for 120 individuals from five localities; the Sendai Bay-Tokyo Bay, the Ise Bay-Mikawa Bay, the Inland Sea-Genai Nada, the Omura Bay and the Ariake Sound-Tachibana Bay. Analyses of MS-DNA and mtDNA revealed a significant population genetic structure that corresponds to the locality. This result is compatible with previous studies based on ecological, morphological and molecular data, therefore, we concluded that there are (at least) five local populations in Japanese waters. All Japanese populations had lower levels of heterozygosity (HO = 0.45-0.55) than those found in Chinese populations. Considering from significant population genetic structure and low genetic diversity, five local populations should be treated as different management units in the design and implications of conservation programs. In addition, levels of genetic differentiation among the local populations based on mtDNA data (FST) are higher than those based on MS-DNA data (RST) and the test of isolation by distance is significant only in MS-DNA, suggesting the existence of male-mediated gene flow of this species. The phylogenetic analysis of the Chinese and the Japanese finless porpoises indicated that the population of Japanese finless porpoises has two diverged haplotypes. Major haplotype cluster is constructed from all of Japanese populations, but the other is mainly constructed from the Ariake Sound-Tachibana Bay population. This may suggest that there are at least two distinct origins of Japanese finless porpoises..
||Seedlings of gymnosperms are able to synthesize chlorophyll even in the dark due to dark-operative protochlorophyllide oxidoreductase (DPOR) encoded by chloroplast DNA. In some conifers RNA-editing occurs in mRNA of chlB encoding one of the DPOR subunits resulting in amino acid substitutions in ChlB. These substitutions would be important for the DPOR activity. However, there has been no experimental evidence. In this study the efficiency of RNA-editing in the chlB mRNA was analyzed in black pine seedlings grown in the light and dark. The ratio of edited chlB mRNA to the total chlB mRNA was significantly higher in the dark grown seedlings than that of seedlings grown in the light. In addition, a cyanobacterial ChlB variant corresponding to the unedited mRNA lost the ability to form the catalytic component, NB-protein (hetero tetramer of ChlN and ChlB). This result indicated that the amino acid substitutions by RNA-editing are essential for the formation of NB-protein. It is suggested that black pine seedlings regulates greening process via DPOR activity by RNA-editing in response to environmental light conditions..
||Figs (Ficus, Moraceae) and their pollinating figwasps (Agaonidae, Chalcidoidea, Hymenoptera) form tight, species-specific obligatory mutualisms, in which neither species can propagate without the other under natural conditions. Figs depend on figwasps for pollen transmission, whereas figwasps complete their growth, development and reproduction within the fig inflorescence. Therefore, dispersal distance and a level of gene flow of one party are expected to affect those of the other party. In this study, we analyzed population structures of Ficus erecta and their pollinating figwasp, Blastophaga nipponica, using SSRs and organelle genome sequence polymorphisms. We used samples from Kansai, Kyushu, Okinawa Island, Yaeyama Islands and Taiwan. Bayesian clustering analyses based on the SSRs data showed that F. erecta and B. nipponica have a similar population structure, which correspond to their locality. In addition, we found a significant correlation between the pairwise Fst values of F. erecta and B. nipponica, suggesting interdependent gene flow of these species. On the other hand, mitochondrial genomic data indicated large genetic differentiations between the Kansai and the other populations in B. nipponica, which is inconsistent to the result of the SSRs data. This may imply that F. erecta and B. nipponica of the Kansai population have different origin-histories. .
||Taxodium distichum is a coniferous tree that is widely distributed in southeastern North America. Although levels of genetic differentiation between its two varieties, bald-cypress and pond-cypress, are low, genetic differentiation between the Mississippi river coast region and Florida region has been shown using SSR markers. In this study, we determined the sequences of T. distichum at 5 nuclear loci using DNA sampled from populations of the Mississippi river coast and Florida regions. High and significant Fst values were found at two loci: between the two varieties at AMT and between the two regions at Acl5. To investigate whether the high Fst value obtained at the AMT locus reveals variety-specific genetic differentiation, we conducted a preliminary simulation study assuming the neutrality of alleles and a simple population structure. The P-value of the observed value at AMT was 0.0495, suggesting a possible contribution of AMT to the differentiation between varieties..
||Dark-operative protochlorophyllide reductase (DPOR) is a nitrogenase-like enzyme consisting of two components L-protein (ChlL) and NB-protein (ChlN-ChlB), and plays a critical role in chlorophyll (Chl) biosynthesis in the dark. All subunits of DPOR are encoded in plastid genomes in photosynthetic eukaryotes. RNA editing in chlN and chlB, by which some codons are converted to encode evolutionarily conserved amino acid residues, was reported in some coniferous species. We examined the effects of the amino acid alteration by RNA-editing on DPOR activity using the cyanobacterial DPOR as a model. We constructed a series of shuttle vectors to express chlN-chlB with and without mutations responsible for the RNA editing, and introduced them into a mutants lacking chlB of cyanobacterium Leptolyngbya boryana. Only the transformants carrying the edited chlN-chlB genes restored the ability of Chl biosynthesis in the dark. Biochemical analysis of the cyanobacterial NB-protein with site-directed mutations responsible for the RNA editing supported the in-vivo complementation result. These results suggested that RNA editing regulates the greening in the dark through the NB-protein activity. .