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Functional Evolutionary genomics: Inferring the origin and function of the genes involved in nodulation symbiosis with nitrogen fixation

Research Project

Project/Area Number 20570220
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Evolutionary biology
Research InstitutionThe University of Tokyo

Principal Investigator

AOKI Seishiro  東京大学, 総合文化研究科, 学術研究員 (10334301)

Co-Investigator(Kenkyū-buntansha) ITO Motomi  東京大学, 大学院総合文化研究科, 教授 (00193524)
Project Period (FY) 2008-04-08 – 2013-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2012: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2011: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2010: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2009: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2008: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords進化 / ゲノム / 共生 / 根粒菌 / マメ科植物 / 分子進化 / 協力行動 / 遺伝子重複 / 水平移行 / ゲノムアイランド / 蛋白質機能 / 生物間相互作用 / マメ / 感染実験 / ゲノム網羅的解析 / 協力 / 分子機能 / 計算 / 生理実験
Research Abstract

There is a possibility that the symbiosis genes with an important role for the nodulation and nitrogen fixation passed through the special evolution that may be different from the other housekeeping genes. We compared the genomic information of various bacteria using the background information of symbiosis with legumes and inferred the new symbiotic nodulation genes and the evolution of this symbiosis. We examined large scale phylogenetic profiling and revealed the evolutionary origin of nodulation genes. Contrary to the widely accepted scenario of the alpha-proteobacterial origin of rhizobia, our exhaustive analysis showed that the nodulation symbiosis of rhizobia with legumes may have originated from beta-proteobacterial family. Furthermore, we found that there was a possibility that several genes which symbiosis function was not known so far are characteristic of root nodule bacteria. We confirm the symbiosis function of these genes by the gene destruction.

Report

(7 results)
  • 2013 Final Research Report ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report   Self-evaluation Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (39 results)

All 2013 2012 2011 2010 2009 2008

All Journal Article (10 results) (of which Peer Reviewed: 7 results) Presentation (23 results) Book (6 results)

  • [Journal Article] From β-to α-Proteobacteria: The origin and evolution of rhizobial nodulation genes nodIJ2013

    • Author(s)
      Seishiro Aoki, Motomi Ito, Wataru Iwasaki
    • Journal Title

      Molecular Biology and Evolution

      Volume: 30 Pages: 2494-2408

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] From β- to α-Proteobacteria: The origin and evolution of rhizobial nodulation genes nodIJ2013

    • Author(s)
      Seishiro Aoki, Wataru Iwasaki, Motomi Ito
    • Journal Title

      Molecular Biology and Evolution

      Volume: 30 Pages: 2494-2408

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genotypic and phenotypic diversity of rhizobia isolated from Lathyrus japonicus indigenous to Japan2010

    • Author(s)
      Seishiro Aoki, Tetsuya Kondo, Danielle Prevost, Sayuri Nakata, Tadashi Kajita, Motomi Ito
    • Journal Title

      Systematic and Applied Microbiology

      Volume: 33 Pages: 383-397

    • Related Report
      2013 Final Research Report 2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamic morphologies of pollen plastids visualised by vegetative-specific FtsZ1-GFP in Arabidopsis thaliana2010

    • Author(s)
      Makoto Fujiwara, HarukiHashimoto, Yusuke Kazama, Tomonari Hirano, Yasushi, Yoshioka, Seishiro Aoki, Naoki Sato, Ryuuichi Itoh, and Tomoko Abe
    • Journal Title

      Protoplasma

      Volume: 242 Pages: 19-33

    • Related Report
      2013 Final Research Report 2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genotypic and phenotypic diversity of rhizobia isolated from Lathyrus japonicus indigenous to Japan.2010

    • Author(s)
      Seishiro Aoki, Tetsuya Kondo, Danielle Prevost, Sayuri Nakata, Tadashi Kajita, Motomi Ito
    • Journal Title

      Systematic and Applied Microbiology 33

      Pages: 383-397

    • Related Report
      2010 Self-evaluation Report
  • [Journal Article] Dynamic morphologies of pollen plastids visualised by vegetative-specific FtsZ1-GFP in Arabidopsis thaliana2010

    • Author(s)
      Makoto Fujiwara, Haruki Hashimoto, Yusuke Kazama, Tomonari Hirano, Yasushi, Yoshioka, Seishiro Aoki, Naoki Sato, Ryuuichi Itoh, Tomoko Abe
    • Journal Title

      Protoplasma 242

      Pages: 19-33

    • Related Report
      2010 Self-evaluation Report
  • [Journal Article] Molecular Adaptation of rbcL in the Heterophyllous Aquatic Plant Potamogeton2009

    • Author(s)
      Satoko Iida, Atsuko Miyagi, Seishiro Aoki, Motomi Ito, Yasuro Kadono, Keiko Kosuge
    • Journal Title

      PLoS ONE

      Volume: 4

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Adaptation of rbcL in the Heterophyllous Aquatic Plant Potamogeton.2009

    • Author(s)
      Satoko Iida, Atsuko Miyagi, Seishiro Aoki, Motomi Ito, Yasuro Kadono, Keiko Kosuge.
    • Journal Title

      PLoS ONE 4

    • Related Report
      2010 Self-evaluation Report
  • [Journal Article] Molecular Adaptation of rbcL in the Heterophyllous Aquatic Plant Potamogeton2009

    • Author(s)
      Iida S, Miyagi A, Aoki S, Ito M, Kadono Y, Kosuge
    • Journal Title

      PLoS ONE

      Volume: 4(2)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular Adaptation of rbcL in the Heterophyllous Aquatic Plant Potamogeton.2009

    • Author(s)
      Iida S, Miyagi A, Aoki S, Ito M, Kadono Y, Kosuge
    • Journal Title

      PLoS ONE 4(2)

      Pages: 4633-4633

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] Model for the evolutionary dynamics of nitrogen fixation in the legume-rhizobia symbiosis2013

    • Author(s)
      Hironori Fujita, Seishiro Aoki, Masayoshi Kawaguchi
    • Organizer
      18th International Congress on Nitrogen Fixation
    • Place of Presentation
      Phoenix Seagaia Resort, Miyazaki
    • Related Report
      2013 Final Research Report 2012 Annual Research Report
  • [Presentation] MOLECULAR EVOLUTIN OF VOLVOCALEAN ACTIN GENES2013

    • Author(s)
      Takako Kato-Minoura, Mika Ehara, Kumiko Karino, Nobuyuki Akimoto, Norito Yoshiga, and Seishiro Aoki
    • Organizer
      Second International Volvox Conference
    • Place of Presentation
      Fredericton, New Brunswick, Canada
    • Related Report
      2012 Annual Research Report
  • [Presentation] Phylogenic analyses have revealed a unique origin of NAP, a Volvocales unconventional actin, in Chlolophyta2012

    • Author(s)
      Takako Kato-Minoura, Kumiko Karino, Nobuyuki Akimoto, Norito Yoshiga, and Seishiro Aoki
    • Organizer
      Joint Meeting of The 45th Annual Meeting of the Japanese Society of Developmental Biologists & The 64th Annual Meeting of the Japan Society for Cell Biology
    • Place of Presentation
      Kobe International Conference Center and The Kobe Chamber of Commerce and Industry, Kobe
    • Related Report
      2012 Annual Research Report
  • [Presentation] マメ科植物-根粒菌相互作用に関わる共生遺伝子の起源とゲノム網羅的な探索2011

    • Author(s)
      青木誠志郎
    • Organizer
      統数研共同利用重点型研究集会
    • Place of Presentation
      統計数理研究所(招待講演)
    • Year and Date
      2011-10-26
    • Related Report
      2011 Annual Research Report
  • [Presentation] 分子進化解析による共生遺伝子の機能進化推定:茎頂分裂組織または根粒形成に関わるCLV1/HAR1遺伝子ファミリーについて2011

    • Author(s)
      青木誠志郎, 川口正代司, 佐藤修正、伊藤元己
    • Organizer
      日本植物学会
    • Place of Presentation
      東京大学
    • Year and Date
      2011-09-17
    • Related Report
      2011 Annual Research Report
  • [Presentation] マメ科植物-根粒菌相互作用に関わる共生遺伝子の起源とゲノム網羅的な探索2011

    • Author(s)
      青木誠志郎
    • Organizer
      共同利用重点型研究による研究集会「ゲノム多様性と進化の統計数理」
    • Place of Presentation
      統計数理研究所、立川
    • Related Report
      2013 Final Research Report
  • [Presentation] 分子進化解析による共生遺伝子の機能進化推定:茎頂分裂組織または根粒形成に関わるCLV1/HAR1遺伝子ファミリーについて2011

    • Author(s)
      青木誠志郎,川口正代司,佐藤修正,伊藤元己
    • Organizer
      日本植物学会第75回大会
    • Place of Presentation
      東京大学、東京都目黒区
    • Related Report
      2013 Final Research Report
  • [Presentation] Genetic and phenotypic diversity of rhizobia isolated from Lathyrus japonicus in Japan and Canada2010

    • Author(s)
      Seishiro Aoki, Motomi Ito
    • Organizer
      Grad.Sch.Arts and Sci.
    • Place of Presentation
      Unuv.Tokyo
    • Year and Date
      2010-12-07
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] Genetic and phenotypic diversity of rhizobia isolated from Lathyrus japonicus in Japan and Canada2010

    • Author(s)
      Seishiro Aoki, Motomi Ito
    • Organizer
      Memorial Symposium for the 26th International Prize for Biology , Biology of Symbiosis
    • Place of Presentation
      Tsukuba International Congress Center, Tsukuba
    • Related Report
      2013 Final Research Report
  • [Presentation] Genetic and phenotypic diversity of rhizobia based on PCR-based identification, RAPD, RFLP, phylogenetic, and physiological analyses isolated from Lathyrus japonicus in Japan and Canada2010

    • Author(s)
      Seishiro Aoki, Motomi Ito
    • Organizer
      1st Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation
    • Place of Presentation
      Aoshima Palm Beach Hotel, Miyazaki
    • Related Report
      2013 Final Research Report
  • [Presentation] Genetic and phenotypic diversity of rhizobia based on PCR-based identification, RAPD, RFLP, phylogenetic, and physiological analyses isolated from Lathyrus japonicus in Japan and Canada2010

    • Author(s)
      Seishiro Aoki, Motomi Ito
    • Organizer
      Grad.Sch.Arts and Sci.
    • Place of Presentation
      Unuv.Tokyo
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] Genetic and phenotypic diversity of rhizobia based on PCR-based identification, RAPD, RFLP, phylogenetic, and physiological analyses isolated from Lathyrus japonicus in Japan and Canada2010

    • Author(s)
      Seishiro Aoki, Motomi Ito
    • Organizer
      1st Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixatior
    • Place of Presentation
      Miyazaki University
    • Related Report
      2010 Annual Research Report
  • [Presentation] 機能進化ゲノミクス:進化解析を用いた共生関連遺伝子のゲノム網羅的探索とその実験的検証2009

    • Author(s)
      青木誠志郎, 下田宜司, 伊藤元己
    • Organizer
      日本植物学会
    • Place of Presentation
      山形大学
    • Year and Date
      2009-09-14
    • Related Report
      2009 Annual Research Report
  • [Presentation] 機能進化ゲノミクス:進化解析を用いた共生関連遺伝子のゲノム網羅的探索とその実験的検証2009

    • Author(s)
      青木誠志郎, 下田宜司, 伊藤元己
    • Organizer
      日本進化学会
    • Place of Presentation
      北海道大学
    • Year and Date
      2009-09-02
    • Related Report
      2009 Annual Research Report
  • [Presentation] 機能進化ゲノミクス:進化解析を用いた共生関連遺伝子のゲノム網羅的探索とその実験的検証2009

    • Author(s)
      青木誠志郎、下田宣司、伊藤元己
    • Organizer
      第11回日本進化学会大会 (札幌大会)
    • Place of Presentation
      北海道大学、札幌
    • Related Report
      2013 Final Research Report
  • [Presentation] マメ科の汎熱帯海流散布植物と根粒菌の共生特異性2009

    • Author(s)
      中田さゆり、青木誠志郎、梶田忠
    • Organizer
      第11回日本進化学会大会 (札幌大会)
    • Place of Presentation
      北海道大学、札幌
    • Related Report
      2013 Final Research Report
  • [Presentation] 機能進化ゲノミクス:進化的特徴の類似性に基づくゲノム網羅的な共生遺伝子の計算推定とその実験的検証2009

    • Author(s)
      青木誠志郎、下田宜司、伊藤元己
    • Organizer
      植物微生物研究会第19回研究交流会
    • Place of Presentation
      あがたの森文化会館、松本市
    • Related Report
      2013 Final Research Report
  • [Presentation] 機能進化ゲノミクス:進化解析を用いた共生関連遺伝子のゲノム網羅的探索とその実験的検証2009

    • Author(s)
      青木誠志郎、下田宜司、伊藤元己
    • Organizer
      日本植物学会73回(山形)大会
    • Place of Presentation
      山形大学、山形
    • Related Report
      2013 Final Research Report
  • [Presentation] 機能進化ゲノミクス:進化解析を用いた共生関連遺伝子のゲノム網羅的探索とその実験的検証2009

    • Author(s)
      青木誠志郎、下田宜司、伊藤元己
    • Place of Presentation
      (1)東大・院・総合文化・広域科学(2)農業生物資源研
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] 機能進化ゲノミクス:進化的特徴の類似性に基づくゲノム網羅的な共生遺伝子の計算推定とその実験的検証2009

    • Author(s)
      青木誠志郎、下田宜司、伊藤元己
    • Organizer
      植物微生物研究会第19回研究交流会
    • Place of Presentation
      東大・院・総合文化、2生物研
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] 機能進化ゲノミクス:進化解析を用いた共生関連遺伝子のゲノム網羅的探索とその実験的検証2009

    • Author(s)
      青木誠志郎、下田宣司、伊藤元己
    • Organizer
      第11回日本進化学会大会(札幌大会)
    • Place of Presentation
      東大・院・総合文化、2生物研
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] 原始的被子植物Amborella trichopodaの花器官形成に関わるMADS-box B機能遺伝子群の解析2009

    • Author(s)
      杉森香代子, 青木誠志郎, 伊藤元己
    • Organizer
      第11回日本進化学会大会(札幌大会)
    • Place of Presentation
      東大・院・総合文化
    • Related Report
      2010 Self-evaluation Report
  • [Presentation] マメ科の汎熱帯海流散布植物と根粒菌の共生特異性2009

    • Author(s)
      中田さゆり、青木誠志郎、梶田忠
    • Organizer
      第11回日本進化学会大会(札幌大会)
    • Place of Presentation
      1千葉大・院・理、2東大・院・総合文化
    • Related Report
      2010 Self-evaluation Report
  • [Book] 「進化学事典」 "51.5植物と真菌類/バクテリアの共進化"2012

    • Author(s)
      日本進化学会創立10周年記念出版編集委員会
    • Publisher
      共立出版
    • Related Report
      2013 Final Research Report
  • [Book] 進化学事典2012

    • Author(s)
      日本進化学会編
    • Total Pages
      996
    • Publisher
      共立出版
    • Related Report
      2012 Annual Research Report
  • [Book] 進化学事典2011

    • Author(s)
      日本進化学会編
    • Total Pages
      996
    • Publisher
      共立出版株式会社
    • Related Report
      2011 Annual Research Report
  • [Book] 「図説生物学」 "11.7花成2花器官の形態形成"2010

    • Author(s)
      東京大学教養学部図説生物学編集委員会編
    • Publisher
      東京大学出版会
    • Related Report
      2013 Final Research Report
  • [Book] 「共進化の生態学」"第7章マメー根粒菌共生系の進化"2008

    • Author(s)
      種生物学会編
    • Publisher
      文一総合出版
    • Related Report
      2013 Final Research Report
  • [Book] 共進化の生態学("第7章マメー根粒菌共生系の進化")(種生物学会編)2008

    • Author(s)
      青木誠志郎
    • Publisher
      文一総合出版
    • Related Report
      2010 Self-evaluation Report

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Published: 2008-04-01   Modified: 2019-07-29  

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