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2013 Fiscal Year Annual Research Report

種内多数全ゲノム解析によるピロリ菌日本株のヒト胃への適応進化機構の解明

Research Project

Project/Area Number 12J00830
Research InstitutionThe University of Tokyo

Principal Investigator

矢原 耕史  東京大学, 大学院新領域創成科学研究科, 特別研究員(PD

Project Period (FY) 2012 – 2014-03-31
Keywordsゲノム / バイオインフォマティクス / 相同組み換え / ホットスポット / 集団ゲノミクス / 病原細菌 / 自然淘汰 / 進化
Research Abstract

まず、ピロリ菌の地理的な集団構造と、集団の垣根を越えた相同組み換えによる遺伝情報のフローを明らかにする研究を完成させた。新たにゲノムの解読された沖縄株を含め、トータルの解析対象の株数を昨年度の約3倍に増加させた上で、欧州で開発されたchromosome paintingとfineSTRUCTURE(当初はヒトゲノム解析のために開発された方法)を、世界で初めて細菌のゲノム解析に応用した。その結果、従来の研究では見出されてこなかった、より細かな集団構造が明らかになると同時に、集団の垣根を越えた遺伝情報のフローの定量的な理解が可能になった(Yahara et al. (2013), Molecular Biology and Evolution)。
次に、英国に長期滞在しながら、細菌ゲノムの中で、自然選択が作用し適応進化に寄与している可能性の高い相同組み換えのホット領域を、100を越える多数のゲノムの塩基配列データから推定する方法の開発に注力した。系統樹に依存せず、クローンの存在に頑健で、相同組み換えの相対強度を一塩基単位で推定可能にするために、予めゲノムを順序付で並び替えた上でchromosome paintingを実行し、ゲノム平均に対する各サイトのコピー確率行列の乖離度を足し込む、というアイディアに基づいて、その開発に成功した。シミュレーションによる性能評価を行った上で、現実のゲノムデータに適用してその有効性を示し、オープンソースのプログラムorderedPainting (https://github.com/bioprojects/orderedPainting)として実装・公開した(Yahara et al. in press, Molecular Biology and Evolution)。

Strategy for Future Research Activity

(抄録なし)

  • Research Products

    (11 results)

All 2014 2013

All Journal Article (2 results) (of which Peer Reviewed: 2 results) Presentation (9 results) (of which Invited: 1 results)

  • [Journal Article] Efficient inference of recombination hot regions in bacterial genomes2014

    • Author(s)
      Koji Yahara, Xavier Didelot, M. Azim Ansari, Samuel K. Sheppard and Daniel Faluah
    • Journal Title

      Molecular Biology and Evolution

      Volume: (印刷中)

    • DOI

      10.1093/molbev/msu082

    • Peer Reviewed
  • [Journal Article] Chromosome painting in silico in a bacterial species reveals fine population structure2013

    • Author(s)
      Koji Yahara, Ynshikazu Furuta, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi
    • Journal Title

      Molecular Biology and Evolution

      Volume: 30(6) Pages: 1454-64

    • DOI

      10.1093/molbev/mst055

    • Peer Reviewed
  • [Presentation] Chromosome painting in silico in a bacterial species reveals fine population structure2014

    • Author(s)
      Koji Yahara, Yoahikazu Furuta, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattari, Ikuo Uchiyama, Ichizo Kobayashi
    • Organizer
      ゲノム微生物学会
    • Place of Presentation
      東京農業大学(東京都)
    • Year and Date
      20140307-09
  • [Presentation] Population genomic and epidemiological studies on microbes and genes2014

    • Author(s)
      Koji Yahara
    • Organizer
      ゲノム微生物学会
    • Place of Presentation
      東京農業大学(東京都)
    • Year and Date
      2014-03-08
    • Invited
  • [Presentation] Chromosome painting in silica in a bacterial species reveals fine population structure2014

    • Author(s)
      Koji Yahara, Yoshikazu Furuta, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi
    • Organizer
      Population Genetic Group 47
    • Place of Presentation
      Bath, UK
    • Year and Date
      2014-01-08
  • [Presentation] Chromosome painting in silico in a bacterial species reveals fine population structure2013

    • Author(s)
      Koji Yahara, Yoshikazu Furuta, Kanshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyarna, Ichizo Kobayashi
    • Organizer
      17th International Workshop on Campylobacter, Helicobacter and Related Organisms
    • Place of Presentation
      Aberdeen, UK
    • Year and Date
      2013-09-19
  • [Presentation] 病原細菌の次世代ゲノムワイド関連解析2013

    • Author(s)
      矢原耕史, Guillaume Meric, XaviIer Didelot, Ana Vidal, Anne Ridley, Felicity Clifton-Hadley, Keith Jolley, Samuel Sheppard
    • Organizer
      統計関連学会連合大会
    • Place of Presentation
      大阪大学(大阪府)
    • Year and Date
      2013-09-10
  • [Presentation] Pathogen survival on the pathway to infection : agenome-wide association study2013

    • Author(s)
      Koji Yahara, Guillaume Meric, Xavier Didelot, Ana Vidal, AnneRidley, Felicity Clifton-Hadley, Keith Jolley, Samuel Sheppard
    • Organizer
      Society for Molecular Biology and Evolution
    • Place of Presentation
      Chicago, USA
    • Year and Date
      2013-07-08
  • [Presentation] Pathogen survival on the pathway to infection : agenome-wide association study2013

    • Author(s)
      Koji Yahara, Guillaume Meric, Xavier Didelot, Ana Vidal, Anne Ridley, Felicity Clifton-Hadley, Keith Jolley, Samuel Sheppard
    • Organizer
      Applied Bioinformatics and Public Health Microbiology
    • Place of Presentation
      Cambridge, UK
    • Year and Date
      2013-05-16
  • [Presentation] Genome-wide survey of homologous recombination and diversifying selection in a highly sexual bacterial species2013

    • Author(s)
      Koji Yahara, Mikihiko Kawai, Yoshikazu Furuta, Noriko Takahashi, Naofumi Handa, Takeshi Tsuru, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi
    • Organizer
      Computational Molecular Evolution
    • Place of Presentation
      Hinxton, UK
    • Year and Date
      2013-05-03
  • [Presentation] Pathogen survival on the pathway to infection : agenome-wide association study2013

    • Author(s)
      Koji Yahara, Guillaume Meric, Xavier Didelot, Ana Vidal, Anne Ridley, Felicity Clifton-Hadley, Keith Jolley, Samuel Sheppard
    • Organizer
      Computational Molecular Evolution
    • Place of Presentation
      Hinxton, UK
    • Year and Date
      2013-05-03

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Published: 2015-07-15  

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