九州大学 研究者情報
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楠見 淳子(くすみ じゆんこ) データ更新日:2019.06.07

准教授 /  比較社会文化研究院 環境変動部門 生物多様性


主な研究テーマ
分子レベルのcompensatory evolution (補償的進化)の理論的研究
キーワード:補償的進化 集団遺伝学
2013.04~2019.03.
広義ヒノキ科樹木、ヌマスギの集団遺伝学解析
キーワード:ヌマスギ、遺伝的多様性、塩基配列多型、マイクロサテライト多型
2007.04~2019.03.
イチジク属植物とイチジクコバチの共生関係と共進化の研究
キーワード:集団遺伝学、分子進化学、分子系統、共進化、共種分化
2008.04~2019.03.
針葉樹のchl遺伝子群の分子進化学的解析
キーワード:分子進化 針葉樹 非光依存型プロトクロロフィリド還元酵素
2005.04~2017.03.
従事しているプロジェクト研究
湿地性針葉樹ヌマスギの水環境適応を担う遺伝子基盤の解明
2016.10, 代表者:楠見淳子, 九州大学
ヌマスギ(Taxodium distichum)の水環境への適応に着目し、環境適応に関わる遺伝子の探索とその進化過程の解明を試みる。ここでは、実生を用いた栽培実験系の確立、遺伝子発現解析に必要なcDNA配列データの収集およびトランスクリプトームの比較解析を行い、研究の基盤となるデータ、実験系の整備を行う。これまであまり知られていない針葉樹の環境適応のメカニズムやその進化過程の遺伝的背景を明らかにすることで、植物の進化研究において重要な知見をもたらすことが期待できる.
ブナ科樹木の繁殖形質多様性を生み出す開花遺伝子の発現制御戦略
2017.04, 代表者:佐竹暁子, 九州大学 理学研究院
送粉様式、結実までの経過時間、 開花季節、花・種子量の年変動の程度など、多様な繁殖形質をもつブナ科樹木を対象に、1 花と 種子生産に必要とされる資源投資量の測定、2 網羅的遺伝子発現解析による遺伝子制御ネットワ ークの推定と種間比較、3 開花遺伝子発現制御の進化モデルの開発と解析、を行うことによって、 繁殖資源分配戦略と開花戦略の多様化メカニズムを遺伝子ネットワーク進化の視点から明らかに し、生活史戦略の進化に関わる至近要因・究極要因の推定をシームレスに行う枠組みを提案する。.
刺胞動物と緑藻との共生の起源・共進化過程の解明
2016.04~2019.03, 代表者:小早川義尚, 九州大学 基幹教育院
日本だけで棲息が確認されている内胚葉上皮細胞内にクロロコッカム(Chlorococcum)を共生させているvulgaris種群のヒドラ(Hydra magnipapillataのJ7系統)とこれまでクロレラ(Chlorella)との共生が詳しく研究されているグリーンヒドラ(viridissima種群、日本での棲息は未確認)を材料に、「刺胞動物と緑藻との共生の起源・共進化過程の解明」を目指して、共生体緑藻と宿主の組み合わせを様々に変えた系統を多数確立し、それぞれの系統について光・温度・栄養条件等による共生状態の変化、増殖率・有性生殖の頻度などの基本的な特徴を明らかにし、比較解析することが本研究の目的の一つである。また、確立した実験系を用いて共生状態の緑藻と単離培養した緑藻、緑藻を共生させているヒドラと共生させていないヒドラについて次世代シークエンサーを用いてそれぞれのトランスクリプトームのデータを得、その比較解析を行い、共生体・宿主双方における「共生に関与する遺伝子の探索」とその発現解析を行うことがもう一つの目的である。.
非モデル生物を用いた異質倍数体形成を介した植物の種分化の分子機構解明
2013.04~2016.03, 代表者:楠見淳子, 九州大学 大学院 比較社会文化研究院
異質倍数体形成を発端とする種分化の遺伝的背景をゲノムワイドな変異解析から解明する。
異質倍数体形成によるゲノムの劇的な変化は、新規形質の創出、親系統との即座の生殖隔離をもたら
すことから、進化、種分化において重要なプロセスであると古くから認識されてきた。申請者は、先
行研究[1]により、小笠原諸島固有のイチジク属植物3種のうち1種は異質倍数体(4倍体)であり、
固有種3種は染色体倍化、雑種形成を経て種分化したことを示した。この小笠原イチジク属植物3種
を材料に、⑴異質倍数体種の遺伝子喪失の頻度、⑵異質倍数体種の遺伝的多様性、⑶小笠原固有種3
種の遺伝的分化の程度、分岐年代、進化速度の推定を行い、雑種形成と染色体倍加を伴った種分化の
遺伝的背景を明らかにする。.
研究業績
主要著書
主要原著論文
1. Natsuki Moriguchi, Kentaro Uchiyama, Ryutaro Miyagi, Etsuko Moritsuka, Aya Takahashi, Koichiro Tamura, Yoshihiko Tsumura, Kosuke M. Teshima, Hidenori Tachida, Junko Kusumi, Inferring the demographic history of Japanese cedar, Cryptomeria japonica, using amplicon sequencing, Heredity, 10.1038/s41437-019-0198-y, 2019.01, [URL], The evolution of a species depends on multiple forces, such as demography and natural selection. To understand the trajectory and driving forces of evolution of a target species, it is first necessary to uncover that species’ population history, such as past and present population sizes, subdivision and gene flow, by using appropriate genetic markers. Cryptomeria japonica is a long-lived monoecious conifer species that is distributed in Japan. There are two main lines (omote-sugi and ura-sugi), which are distinguished by apparent differences in morphological traits that may have contributed to their local adaptation. The evolution of these morphological traits seems to be related to past climatic changes in East Asia, but no precise estimate is available for the divergence time of these two lines and the subsequent population dynamics in this species. Here, we analyzed the nucleotide variations at 120 nuclear genes in 94 individuals by using amplicon sequencing in combination with high-throughput sequencing technologies. Our analysis indicated that the population on Yakushima Island, the southern distribution limit of C. japonica in Japan, diverged from the other populations 0.85 million years ago (MYA). The divergence time of the other populations on mainland Japan was estimated to be 0.32 MYA suggesting that the divergence of omote-sugi and ura-sugi might have occurred before the last glacial maximum. Although we found modest levels of gene flow between the present populations, the long-term isolation and environmental heterogeneity caused by climatic changes might have contributed to the differentiation of the lines and their local adaptation..
2. Junko Kusumi, Motoshi Ichinose, Masaru Iizuka, Effects of gene duplication, epistasis, recombination and gene conversion on the fixation time of compensatory mutations, Journal of Theoretical Biology, 10.1016/j.jtbi.2019.02.001, 467, 134-141, 2019.04, [URL], Gene duplication is one of the major mechanisms of molecular evolution. Gene duplication enables copies of a gene to accumulate mutations through functional redundancy. If a gene encodes a specific protein that interacts with other proteins, RNA, or DNA, the relaxation of selective constraints caused by gene duplication might contribute to the fixation of compensatory mutations that occur at the interacting sites. In this study, we investigate the effect of gene duplication, epistasis among the duplicated copies and gene conversion on the fixation time of compensatory mutations by extending the original model of compensatory evolution proposed by Kimura in 1985. Our simulation results reveal that the time to fixation of compensatory mutations can be decreased remarkably by gene duplication if one of the duplicated loci can completely mask the deleterious effects of a mutation that occurs at the other locus. Conversely, the fixation time can be increased by gene duplication if such functional compensation is weak. We also show that the combination of the degree of functional compensation and the rate of gene conversion between duplicate loci have contrasting effects on the time to fixation of compensatory mutations..
3. Yuka Ikezaki, Yoshihisa Suyama, Beth A. Middleton, Yoshihiko Tsumura, Kosuke Teshima, Hidenori Tachida, Junko Kusumi, Inferences of population structure and demographic history for Taxodium distichum, a coniferous tree in North America, based on amplicon sequencing analysis, American journal of Botany, 10.3732/ajb.1600046, 103, 11, 2016.12, PREMISE OF THE STUDY: Studies of natural genetic variation can elucidate the genetic basis of phenotypic variation and the past population structure of species. Our study species, Taxodium distichum, is a unique conifer that inhabits the ood plains and swamps of North America. Morphological and eco- logical di erences in two varieties, T. distichum var. distichum (bald cypress) and T. distichum var. imbricarium (pond cypress), are well known, but little is known about the level of genetic di erentiation between the varieties and the demographic history of local populations.
METHODS: We analyzed nucleotide polymorphisms at 47 nuclear loci from 96 individuals collected from the Mississippi River Alluvial Valley (MRAV), and Gulf Coastal populations in Texas, Louisiana, and Florida using high-throughput DNA sequencing. Standard population genetic statistics were calculated, and demographic parameters were estimated using a composite-likelihood approach.
KEY RESULTS: Taxodium distichum in North America can be divided into at least three genetic groups, bald cypress in the MRAV and Texas, bald cypress in Florida, and pond cypress in Florida. The levels of genetic di erentiation among the groups were low but signi cant. Several loci showed the signatures of positive selection, which might be responsible for local adaptation or varietal di erentiation.
CONCLUSIONS: Bald cypress was genetically di erentiated into two geographical groups, and the boundary was located between the MRAV and Florida. This di erentiation could be explained by population expansion from east to west. Despite the overlap of the two varieties’ ranges, they were genetically di erentiated in Florida. The estimated demographic parameters suggested that pond cypress split from bald cypress during the late Miocene..
4. Junko Kusumi, Motoshi Ichinose, Masasuke Takefu, Robert Piskol, Wolfgang Stephan, Masaru Iizuka, A model of compensatory molecular evolution involving multiple sites in RNA molecules, Journal of Theoretical Biology, doi:10.1016/j.jtbi.2015.10.008, 388, 96-107, 2016.01, Consider two sites under compensatory fitness interaction, such as a Watson–Crick base pair in an RNA helix or two interacting residues in a protein. A mutation at any one of these two sites may reduce the fitness of an individual. However, fitness may be restored by the occurrence of a second mutation at the other site. Kimura modeled this process using a two-locus haploid fitness scheme with two alleles at each locus. He predicted that compensatory evolution following this model is very rare unless selection against the deleterious single mutations is weak and linkage between the interacting sites is tight. Here we investigate the question whether the rate of compensatory evolution increases if we take the context of the two directly interacting sites into account. By “context”, we mean the effect of neighboring sites in an RNA helix. Interaction between the focal pair of sites under consideration and the context may lead to so-called indirect compensation. Thus, extending Kimura׳s classical model of compensatory evolution, we study the effects of both direct and indirect compensation on the rate of compensatory evolution. It is shown that the effects of indirect compensation are very strong. We find that recombination does not slow down the rate of compensatory evolution as predicted by the classical model. Instead, compensatory substitutions may be relatively frequent, even if linkage between the focal interacting sites is loose, selection against deleterious mutations is strong, and mutation rate is low. We compare our theoretical results with data on RNA secondary structures from vertebrate introns..
5. Junko Kusumi, Yoshihiko Tsumura, Hidenori Tachida, Evolutionary rate variation in two conifer species, Taxodium distichum (L.) Rich. var. distichum (baldcypress) and Cryptomeria japonica (Thunb. ex L.f.) D. Don (Sugi, Japanese cedar), Genes & Genetic Systems, http://doi.org/10.1266/ggs.14-00079, 90, 305-315, 2015.12, With the advance of sequencing technologies, large-scale data of expressed sequence tags and full-length cDNA sequences have been reported for several conifer species. Comparative analyses of evolutionary rates among diverse taxa provide insights into taxon-specific molecular evolutionary features and into the origin of variation in evolutionary rates within genomes and between species. Here, we estimated evolutionary rates in two conifer species, Taxodium distichum and Cryptomeria japonica, to illuminate the molecular evolutionary features of these species, using hundreds of genes and employing Chamaecyparis obtusa as an outgroup. Our results show that the mutation rates based on synonymous substitution rates (dS) of T. distichum and C. japonica are approximately 0.67×10-9 and 0.59×10-9/site/year, respectively, which are 15-25 times lower than those of annual angiosperms. We found a significant positive correlation between dS and GC3. This implies that a local mutation bias, such as context dependency of the mutation bias, exists within the genomes of T. distichum and C. japonica, and/or that selection acts on synonymous sites in these species. In addition, the means of the ratios of synonymous to nonsynonymous substitution rate in the two species are almost the same, suggesting that the average intensity of functional constraint is constant between the lineages. Finally, we tested the possibility of positive selection based on the site model, and detected one candidate gene for positive selection..
6. Junko Kusumi, Zhi-Hui Su, Isolation and characterization of 15 polymorphic microsatellite markers for the fig-pollinating wasp, Blastophaga nipponica (Hymenoptera: Agaonidae), Applied Entomology and Zoology, 10.1007/s13355-014-0267-x, 2014.04, We developed microsatellite markers for the fig-pollinating wasp Blastophaga nipponica Grandi using a dual-suppression-PCR technique. Twenty-one candidates of microsatellite loci were obtained, of which 15 yielded scorable patterns. The degree of polymorphism for the 15 loci was further characterized using summary statistics describing the genetic variation in 60 individuals from three natural populations in Japan. All 15 loci were polymorphic and yielded 2–27 alleles per locus. Overall observed heterozygosity (HO) and expected heterozygosity(HE) were 0.465 and 0.631, respectively. As expected,based on the inbreeding tendency of this species, the mean inbreeding coefficient (FIS) was high (= 0.255). These markers will contribute to studies on the population structure of this species..
7. Motoshi Ichinose, Masaru Iizuka, Junko Kusumi, Masasuke Takefu, Models of compensatory molecular evolution: Effects of back mutation, JOURNAL OF THEORETICAL BIOLOGY, 10.1016/j.jtbi.2013.01.011, 323, 1-10, 2013.01, Compensatory mutations are individually deleterious but appropriate combinations of mutants are harmless. For several models of compensatory molecular evolution, we consider the effects of back mutation. It is shown that the effects of back mutation on the rate of compensatory molecular evolution are weak. Further we estimate the values of selection parameter of deleterious single mutants for the models of compensatory molecular evolution both with and without back mutation using sequence data of folded RNA molecules and compare them with previous results..
8. Ayako Tanaka & Masato Ohtani & Yoshihisa Suyama & Nobuyuki Inomata & Yoshihiko Tsumura & Beth A. Middleton & Hidenori Tachida & Junko Kusumi, Population genetic structure of a widespread coniferous tree, Taxodium distichum [L.] Rich. (Cupressaceae), in the Mississippi River Alluvial Valley and Florida, Tree Genetics & Genomes, 2012.03, Studies of genetic variation can elucidate the structure
of present and past populations aswell as the genetic basis
of the phenotypic variability of species. Taxodium distichum is
a coniferous tree dominant in lowland river flood plains and
swamps of the southeastern USA which exhibits morphological
variability and adaption to stressful habitats. This study
provides a survey of the Mississippi River Alluvial Valley
(MAV) and Florida to elucidate their population structure and
the extent of genetic differentiation between the two regions
and sympatric varieties, including bald cypress (var. distichum)
and pond cypress (var. imbricatum). We determined
the genotypes of 12 simple sequence repeat loci totaling 444
adult individuals from 18 natural populations. Bayesian clustering
analysis revealed high levels of differentiation between
the MAV and the Florida regions. Within the MAV region,
there was a significant correlation between genetic and geographical
distances. In addition, we found that there was
almost no genetic differentiation between the varieties. Most
genetic variation was found within individuals (76.73 %),
1.67 % among individuals within population, 15.36 % among
populations within the regions, and 9.23 % between regions
within the variety. Our results suggest that (1) the populations
of theMAVand the Florida regions are divided into two major
genetic groups, which might originate from different glacial
refugia, and (2) the patterns of genetic differentiation and
phenotypic differentiation were not parallel in this species..
9. Junko Kusumi; Hiroshi Azuma; Hsy-Yu Tzeng; Lien-Siang Chou; Yan-Qiong Peng; Keiko Nakamura; Zhi-Hui Su, Phylogenetic analyses suggest a hybrid origin of the figs (Moraceae: Ficus) that are endemic to
the Ogasawara (Bonin) Islands, Japan, Molecular Phylogenetics and Evolution, http://dx.doi.org/10.1016/j.bbr.2011.03.031, 63, 1, 168-179, 2012.01, The Ogasawara Islands are oceanic islands and harbor a unique endemic flora. There are
three fig species (Ficus boninsimae, F. nishimurae and F. iidaiana) endemic to the Ogasawara Islands,
and these species have been considered to be closely related to Ficus erecta, and to have diverged
within the islands. However, this hypothesis remains uncertain. To investigate this issue, we assessed
the phylogenetic relationships of the Ogasawara figs and their close relatives occurring in Japan,
Taiwan and South China based on six plastid genome regions, nuclear ITS region and two nuclear
genes. The plastid genome-based tree indicated a close relationship between the Ogasawara figs and F.
erecta, whereas some of the nuclear gene-based trees suggested this relationship was not so close. In
addition, the phylogenetic analyses of the pollinating wasps associated with these fig species based on
the nuclear 28S rRNA and mitochondrial cytB genes suggested that the fig-pollinating wasps of F.
erecta are not sister to those of the Ogasawara figs. These results suggest the occurrence of an early
hybridization event(s) in the lineage leading to the Ogasawara figs..
10. Junko Kusumi, Zidong, Li, Tomoyuki Kado, Yoshihiko Tsumura, Beth A. Middleton and Hidenori Tachida, Multilocus patterns of nucleotide polymorphism and demographic change in Taxodium distichum (Cupressaceae) in the lower Mississippi River alluvial valley, American journal of botany, 10.3732/ajb.1000082, 97, 11, 1848-1857, 2010.11.
11. Junko Kusumi、Aya Sato、Hidenori Tachida, Relaxation of Functional Constraint on Light-Independent Protochlorophyllide Oxidoreductase in Thuja, Molecular Biology and Evolution, 10.1093/molbev/msj097, 23, 5, 941-948, Relaxation of Functional Constraint on Light-Independent Protochlorophyllide Oxidoreductase in Thuja, 2006.05.
12. Junko Kusumi and Hidenori Tachida, Compositional properties of green-plant plastid genomes., Journal of Molecular evolution, 10.1007/s00239-004-0086-8, 60, 4, 417-425, 2005.04.
13. Junko Kusumi, Yoshihiko Tsumura, Hiroshi Yoshimaru and Hidenori Tachida, Molecular evolution of nuclear genes in Cupressaceae, a group of conifer trees., Molecular biology and evolution, 19, 5, 736-747, 2002.10.
主要学会発表等
1. 池崎 由佳, 手島 康介, 陶山 佳久, Beth A. Middleton, 津村 義彦, 舘田 英典, 楠見 淳子, アンプリコンシークエンス解析による針葉樹ヌマスギの集団構造解析, 日本進化学会第18回大会, 2016.08, ヌマスギは沼や河川域に生息する湿地性針葉樹である。 ヌマスギの3変種のうちbald-cypressとpond-cypressは北アメリカ南東部において分布が重なっており、形態や生育環境に違いはあるものの遺伝的分化の程度は低いとされてきた。一方、bald-cypressは先行研究(SSR解析)によりミシシッピ川沿岸部とフロリダとの間で地域間分化が示唆されている。本研究では、2変種(bald-cypress, pond-cypress)を含む、3地域(Texas, Mississippi River, Florida)、12集団96個体を用い、48核遺伝子座の塩基配列多型から変種間、地域間分化の程度を推定した。STRUCTUREプログラムによる集団構造解析から、ヌマスギは3つの遺伝的グループ(Bald_Mississippi&Texas, Bald_Florida, Pond_Florida)に分かれることが示された。AMOVAを使い分化の程度を調べたところ、平均的には変種間が地域間よりも高い固定指数値(FCT)を示した。これは、変種間では5つの遺伝子座でFCTが0.2を超える値を持つことによる。また、分化に貢献する適応候補遺伝子を探すため、Arlequin及びBayescanプログラムを用いたFSTのoutlier検出を行ったところ、地域間・変種間でそれぞれ4つの候補遺伝子が検出された。.
2. 楠見 淳子, 舘田 英典, 針葉樹ヌマスギ、スギの進化速度, 日本遺伝学会第86回大会, 2014.09, 針葉樹は巨大なゲノムサイズ、膨大な非コード領域の蓄積など被子植物とは異なるゲノムの特徴を有しており、植物の進化学的研究において興味深い材料である。本研究では、スギ、ヌマスギの189核遺伝子の非同義、同義置換率及びその比(ω)を推定した。同義置換を中立と仮定すると、ヌマスギ、スギそれぞれの年あたりの突然変異率は0.67×10-9/site/year、0.59×10-9/site/yearと推定された。これは草本性双子葉植物の1/25〜1/15に相当する。また、ωの平均値はスギ、ヌマスギでそれぞれ0.106, 0.107となり、平均的には2種は同程度の制約のもとで進化していることが示唆された。.
3. 浦志 知恵, 楠見 淳子, 蘇 智慧, 小笠原固有イチジク属植物の起源, 第16回日本進化学会年会, 2014.08, イチジク属植物とイチジクコバチ類は互恵性の高い種特異的な相利共生関係にあり、共進化・共種分化しているといわれている。本研究では、小笠原固有のイチジク属植物3種 オオヤマイチジク(Ficus iidaiana)、 オオトキワイヌビワ(F. nishimurae)、トキワイヌビワ (F. boninsimae) の起源を明らかにすることを目的として、日本、台湾に分布する近縁種を含めた分子系統解析を行った。葉緑体DNAの解析では日本に分布するイヌビワ(F. erecta)が小笠原固有種3種に最も近縁であることが示されたが、核遺伝子ではイヌビワとオオトキワイヌビワ、トキワイヌビワは姉妹群を形成しなかった。4倍体種であるオオヤマイチジクでは、複数の遺伝子座でイヌビワに近縁な遺伝子と、他の小笠原固有種に近縁な遺伝子が同一個体のゲノム中に存在しており、雑種形成と倍数化を経て種形成されたことが示唆された。また、トキワイヌビワから採取されたイチジクコバチ (Blastophaga sp. ) の系統的位置について解析したところ、中国南西部、東南アジアに分布するコバチと近縁であることが示唆された。.
4. 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. .
5. 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. [1] 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. .
6. 池崎 由佳, 手島 康介, 陶山 佳久, Beth A. Middleton, 津村 義彦, 舘田 英典, 楠見 淳子, 次世代シーケンサーを用いた針葉樹ヌマスギの集団構造に関する多個体、多遺伝子座での解析, 日本遺伝学会第85回大会, 2013.09, ヌマスギは北米南東部に広く分布する針葉樹で、二種類の変種bald cypressとpond cypressが存在する。本研究ではミシシッピ川沿岸部、フロリダ、テキサスの2変種を含む12集団96個体を用い、48核遺伝子座の配列を次世代シーケンサー(454 GS FLX)により決定した。quality controlの結果から、総read数の76.3%のreadを用い、重複遺伝子と思われる遺伝子を除いた37遺伝子の解析を行った。その結果、平均π(total)の値は0.00427であった。固定指数(Fst)は、生育地域間で0.0391、変種間で0.0376であり共に分化の程度は低いことを示した。.
7. 山本 治樹, 楠見 淳子, 藤田 祐一, クロマツPinus thunbergiiにおけるRNA編集による光環境に応答したプロトクロロフィリド還元酵素の活性調節, 日本植物生理学会, 2013.03, 裸子植物の芽生えは、葉緑体DNAにコードされる暗所作動型プロトクロロフィリド還元酵素(DPOR)の活性により暗所においてもクロロフィルを合成し、緑化することができる。いくつかの裸子植物ではDPORのサブユニットをコードする遺伝子の1つchlBにおいてRNA編集による転写後修飾を受けることが報告されている。RNA編集による塩基置換を介したChlBのアミノ酸置換は、DPORの機能発現に重要な意味をもつと推察されているが、その実験的根拠は得られていない。本研究では、明所もしくは暗所で生育したクロマツPinus thunbergiiの実生における、DPORの3つのサブユニット遺伝子chlL, chlN, chlBの発現量、chlBのmRNAにおけるRNA編集の効率の解析を行った。その結果、暗所においてDPOR遺伝子の発現量、およびchlBのRNA編集効率が明所に比べ有意に高いことが確認された。また、RNA編集前のアミノ酸配列をもつ変異ChlBはDPORの触媒コンポーネントNB蛋白質(ChlNとChlBのヘテロ4量体)を形成しないことが明らかとなった。この結果は、RNA編集によるアミノ酸置換はNB蛋白質の形成を介し、DPORの活性を制御していることを示唆している。クロマツの実生では環境の光条件に応答したchlBのRNA編集の効率変化によりDPOR活性を制御し緑化を調節していると考えられる。.
8. 池崎由佳, 陶山 佳久, 津村 義彦, Beth A. Middleton, 舘田 英典, 楠見 淳子, 北米産針葉樹ヌマスギ2 変種間の遺伝的分化に関する核遺伝子の塩基配列分析, 日本遺伝学会, 2012.09, SSRマーカーを用いた解析により、北米南東部に分布する針葉樹ヌマスギの2変種bald cypressとpond cypressの間の遺伝的分化の程度は低く、むしろ主要分布域であるミシシッピ川沿岸部とフロリダ地域の間に有意な分化が認められている。本研究では、両地域の2変種のサンプル(13集団、135個体)を用い、5核遺伝子座の配列を決定し解析した。その結果、AMT遺伝子座では変種間に高い固定指数(Fst)が検出された。AMTでのFst値が変種間の分化によるものかを検討するため中立モデルを使って検定したところ、観測値のP値は0.0495となり、AMT遺伝子が変種間分化に寄与している可能性が示唆された。.
9. 楠見 淳子, 蘇 智慧, イヌビワ(Ficus erecta)と送粉コバチ(Blastophaga nipponica)の集団構造及び遺伝子流動の比較解析, 日本遺伝学会第84回大会, 2012.09, イチジク属植物とイチジクコバチ類の送粉共生系は種特異性が高く、相互に依存した繁殖システムを持つ。従って、それぞれの分散や地域集団間の遺伝子流動の程度は互いに影響しあうことが予想される。本研究では、日本と台湾のイヌビワ、イヌビワコバチを用い、SSR多型及びオルガネラゲノムの塩基配列多型解析を行い、両者の遺伝的集団構造を比較した。SSRの解析では、イヌビワとイヌビワコバチの集団構造がほぼ一致しており、両者の2集団間のFstの値に有意な正の相関があることが示された。一方、ミトコンドリア塩基配列多型から推定されたイヌビワコバチの遺伝的分化のパターンは、SSR多型の結果とは一部矛盾する結果が得られた。.
10. 楠見淳子・蘇智慧, イチジク属植物、送粉コバチ、寄生コバチの種レベルでの遺伝的分化の比較, 日本応用動物昆虫学会, 2011.03.
11. 楠見淳子、蘇智慧, 小笠原産イチジク属固有種の起源, 日本遺伝学会, 2009.09.
学会活動
所属学会名
Society for Molecular Biology &Evolution
日本進化学会
日本遺伝学会
学協会役員等への就任
2015.04~2016.12, 日本遺伝学会, 評議員.
学会大会・会議・シンポジウム等における役割
2012.09.24~2012.09.26, 日本遺伝学会, 座長(Chairmanship).
2012.09.24~2012.09.26, 日本遺伝学会, プログラム委員.
学術論文等の審査
年度 外国語雑誌査読論文数 日本語雑誌査読論文数 国際会議録査読論文数 国内会議録査読論文数 合計
2019年度      
2018年度      
2016年度      
2015年度      
2014年度      
2013年度      
2012年度      
2011年度      
2010年度      
その他の研究活動
海外渡航状況, 海外での教育研究歴
国立中興大学森林学系, Taiwan, 2014.03~2014.03.
研究資金
科学研究費補助金の採択状況(文部科学省、日本学術振興会)
2019年度~2021年度, 基盤研究(C), 代表, microRNAとそのターゲット遺伝子間に生じる補償的進化の検証.
2016年度~2018年度, 基盤研究(C), 代表, 湿地性針葉樹ヌマスギの水環境適応を担う遺伝子基盤の解明.
2016年度~2018年度, 基盤研究(C), 分担, 刺胞動物と緑藻との共生の起源・共進化過程の解明.
2014年度~2016年度, 基盤研究(B), 分担, アンプリコンシークエンス解析を用いた樹木集団進化に関する集団遺伝学的研究.
2013年度~2015年度, 挑戦的萌芽研究, 代表, 非モデル生物を用いた異質倍数体形成を介した植物の種分化の分子機構解明.
日本学術振興会への採択状況(科学研究費補助金以外)
2007年度~2009年度, 特別研究員, 代表, 欠失変異体の適応度データに基づく遺伝子欠失の進化過程の解析.

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