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2013 Fiscal Year Final Research Report

Studies on features and frequencies of recombination in bacterial evolution

Research Project

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Project/Area Number 23651183
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Genome biology
Research InstitutionTohoku University

Principal Investigator

OHTSUBO Yoshiyuki  東北大学, 生命科学研究科, 助教 (40342761)

Project Period (FY) 2011 – 2013
Keywordsrecombination / ShortReadManager / illumina
Research Abstract

To clarify features and frequencies of bacterial recombinational events, two closely related bacterial strains were mixed and incubated in a sterile soil sample. After a long period of incubation cells were recovered on a solid medium, and subjected to illumina sequencing. The illumina sequencing reads were analyzed by developing and using a computational tool named 'ShortReadManager', which is now released at http://www.ige.tohoku.ac.jp/joho/gf/index.php, and I found no evidence that indicates recombination between the two strains.
On the other hand, mutated DNA fragment of 16S ribosomal RNA gene was inserted into a genome of a soil bacteria, in which 5 copies of rRNA gene are present. The mutated fragment was expected to be replaced by the wild-type copy. By quantitative PCR analysis, we found a evidence that suggests concerted evolution of multi gene family.

  • Research Products

    (26 results)

All 2014 2013 2012 2011 Other

All Journal Article (13 results) (of which Peer Reviewed: 13 results) Presentation (10 results) Book (2 results) Remarks (1 results)

  • [Journal Article] Complete Genome Sequence of Pseudomonas sp. Strain TKP, Isolated from a gamma-Hexachlorocyclohexane-Degrading Mixed Culture2014

    • Author(s)
      Ohtsubo Y, Kishida K, Sato T, Tabata M, Kawasumi T, Ogura Y, Hayashi T, Tsuda M, Nagata Y
    • Journal Title

      Genome announcements

      Volume: 2 Pages: e01241-13.

    • DOI

      10.1128/genomeA.01241-13

    • Peer Reviewed
  • [Journal Article] Complete Genome Sequence of the Thermophilic Polychlorinated Biphenyl Degrader Geobacillus sp. Strain JF8 (NBRC 109937)2014

    • Author(s)
      Shintani M, Ohtsubo Y, Fukuda K, Hosoyama A, Ohji S, Yamazoe A, Fujita N, Nagata Y, Tsuda M, Hatta T, Kimbara K
    • Journal Title

      Genome announcements

      Volume: 2 Pages: e01213-13

    • DOI

      10.1128/genomeA.01213-13

    • Peer Reviewed
  • [Journal Article] Complete Genome Sequence of Pseudomonas aeruginosa MTB-1, Isolated from a Microbial Community Enriched by the Technical Formulation of Hexachlorocyclohexane2014

    • Author(s)
      Ohtsubo Y, Sato T, Kishida K, Tabata M, Ogura Y, Hayashi T, Tsuda M, Nagata Y
    • Journal Title

      Genome announcements

      Volume: 2 Pages: e01130-13

    • DOI

      10.1128/genomeA.01130-13

    • Peer Reviewed
  • [Journal Article] Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes2014

    • Author(s)
      Mori H, Maruyama F, Kato H, Toyoda A, Dozono A, Ohtsubo Y, Nagata Y, Fujiyama A, Tsuda M, Kurokawa K
    • Journal Title

      DNA Res

      Volume: 21 Pages: 217-227

    • DOI

      10.1093/dnares/dst052

    • Peer Reviewed
  • [Journal Article] Complete Genome Sequence of Ralstonia pickettii DTP0602, a 2, 4, 6-Trichlorophenol Degrader2013

    • Author(s)
      Ohtsubo Y, Fujita N, Nagata Y, Tsuda M, Iwasaki T, Hatta T
    • Journal Title

      Genome announcements

      Volume: 1 Pages: e00903-13

    • DOI

      10.1128/genomeA.00903-13

    • Peer Reviewed
  • [Journal Article] Inhibitory effect of Pseudomonas putida nitrogen-related phosphotransferase system on conjugative transfer of IncP-9 plasmid from Escherichia coli2013

    • Author(s)
      Inoue K, Miyazaki R, Ohtsubo Y, Nagata Y, Tsuda M
    • Journal Title

      FEMS microbiology letters

      Volume: 345 Pages: 102-109

    • DOI

      10.1111/1574-6968.12188

    • Peer Reviewed
  • [Journal Article] Complete genome sequence of the・ -hexachlorocyclohexane-degrading bactrium Sphingomonas sp. stain MM-12013

    • Author(s)
      Tabata, M., Y. Ohtsubo, S. Ohhata, M. Tsuda, and, Y. Nagata
    • Journal Title

      Genome Announcements

      Volume: 1 (3) Pages: e00247-13

    • DOI

      10.1128/genomeA.00247-13

    • Peer Reviewed
  • [Journal Article] 機能相補による芳香族化合物複合汚染土壌からの新規分解酵素遺伝子の検索2013

    • Author(s)
      永山浩史, 菅原智詞, 遠藤諒, 加藤広海, 大坪嘉行, 永田裕二, 津田雅孝
    • Journal Title

      Journal of Environmental Biotechnology

      Volume: 13 (1) Pages: 51-56

    • Peer Reviewed
  • [Journal Article] Coinetgrate-resolution of toluene-catabolic transposon Tn46512013

    • Author(s)
      Yano, H., H. Genka, Y. Ohtsubo, Y. Nagata, E.M. Top, M. Tsuda
    • Journal Title

      Plasmid

      Volume: 69 Pages: 24-35

    • DOI

      10.1016/j.plasmid.2012.07.004

    • Peer Reviewed
  • [Journal Article] Complete genome sequence of Acidovorax sp. KKS102, a polychlorinated biphenyl-degrading strain2012

    • Author(s)
      Ohtsubo Y, Maruyama F, Mitsui H, Nagata Y, Tsuda M
    • Journal Title

      J Bacteriol

      Volume: 194 Pages: 6970-6971

    • DOI

      10.1128/JB.01848-12

    • Peer Reviewed
  • [Journal Article] Conjugal transfer of polychlorinated biphenyl/biphenyl degradation genes in Acidovorax sp. strain KKS102, which are located on an integrative and conjugative element2012

    • Author(s)
      Ohtsubo Y., Y. Ishibashi, H. Naganawa, S. Hirokawa, S. Atobe, Y. Nagata, M. Tsuda
    • Journal Title

      J Bacteriol

      Volume: 194 Pages: 4237-4248

    • DOI

      10.1128/JB.00352-12

    • Peer Reviewed
  • [Journal Article] Suppression of pleiotropic phenotypes of a Burkholderia multivorans fur mutant by oxyR mutation2012

    • Author(s)
      Kimura A, Yuhara S, Ohtsubo Y, Nagata Y, Tsuda M
    • Journal Title

      Microbiology

      Volume: 158 Pages: 1284-1293

    • DOI

      10.1099/mic.0.057372-0

    • Peer Reviewed
  • [Journal Article] Genomic organization and genomic structural rearrangements of SphingobiumjaponicumUT26, an archetypal gamma- hexachlorocyclohexane- degrading bacterium2011

    • Author(s)
      Nagata, Y., S. Natsui, R. Endo, Y. Ohtsubo, N. Ichikawa, A. Ankai, A. Oguchi, S. Fukui, N. Fujita, and M. Tsuda
    • Journal Title

      Enzyme and Microbial Technology

      Volume: 49 Pages: 499-508

    • Peer Reviewed
  • [Presentation] 環境細菌の PCB 分解能を司る遺伝因子の解析と各種ゲノム解析ソフトウエアの開発2014

    • Author(s)
      大坪 嘉行
    • Organizer
      日本農芸化学会 2014年大会
    • Place of Presentation
      東京
    • Year and Date
      20140327-30
  • [Presentation] FinishChecker : 完全決定したつもりのゲノム配列のチェック機能2014

    • Author(s)
      大坪嘉行, 永田裕二, 津田雅孝
    • Organizer
      日本農芸化学会 2014年大会
    • Place of Presentation
      東京
    • Year and Date
      20140327-30
  • [Presentation] Finish したゲノム配列のチェックツール : FinishChecker2014

    • Author(s)
      大坪嘉行, 永田裕二, 津田雅孝
    • Organizer
      第8回日本ゲノム微生物学会
    • Place of Presentation
      東京
    • Year and Date
      20140307-10
  • [Presentation] フィニッシング支援ツール GenoFinisher とAceFileViewer2013

    • Author(s)
      大坪 嘉行, 永田 裕二, 津田 雅孝
    • Organizer
      農芸化学会 2013年度大会
    • Place of Presentation
      仙台
    • Year and Date
      20130327-28
  • [Presentation] GenomeMatcher 等ウェット研究者向けツール2013

    • Author(s)
      大坪嘉行
    • Organizer
      第7回日本ゲノム微生物学会
    • Place of Presentation
      長浜バイオ大学(長浜)
    • Year and Date
      20130308-10
  • [Presentation] Finishing関連の3つのツール : GenoFinisher, AceFileViewer, ShortReadManager2013

    • Author(s)
      大坪嘉行, 永田裕二, 津田雅孝
    • Organizer
      第7回日本ゲノム微生物学会
    • Place of Presentation
      長浜バイオ大学(長浜)
    • Year and Date
      20130308-10
  • [Presentation] フィニッシング用のツールGenoFinisher の開発2012

    • Author(s)
      大坪嘉行
    • Organizer
      第85回日本細菌学会
    • Place of Presentation
      長崎
    • Year and Date
      20120327-29
  • [Presentation] フィニッシング用のツール GenoFinisherの開発2012

    • Author(s)
      大坪 嘉行, 奥野 周, 永田 裕二, 津田雅孝
    • Organizer
      農芸化学会 2012年度大会
    • Place of Presentation
      京都
    • Year and Date
      20120323-26
  • [Presentation] 微生物ドラフトゲノムのフィニッシングツール GenoFinisher2012

    • Author(s)
      大坪 嘉行, 奥野 周, 永田 裕二, 津田雅孝
    • Organizer
      第6回日本ゲノム微生物学会
    • Place of Presentation
      東京
    • Year and Date
      20120310-12
  • [Presentation] Development of a computational tool for finishing of draft genomic sequence2011

    • Author(s)
      Yoshiyuki Ohtsbuo, et al
    • Organizer
      International Union of Microbiological Societies 2011 Congress
    • Place of Presentation
      Sapporo, Japan
    • Year and Date
      20110906-10
  • [Book] Mobile catabolic genetic elements in pseudomonads. In: Nojiri, H., M. Tsuda, M. Fukuda, and Y. Kamagata (eds), Biodegradative Bacteria: How Bacteria Degrade, Survive, Adapt, and Evolve2014

    • Author(s)
      Tsuda, M., Y. Ohtsubo, and H. Yano
    • Total Pages
      83-103
    • Publisher
      Springer, Tokyo
  • [Book] Strategies to reveal genomic function in natural soil systems. In: Nojiri H, Tsuda M, Fukuda M, Kamagata Y (eds) Biodegradative Bacteria2014

    • Author(s)
      Ohtsubo Y, Nishiyama E, Ishibashi Y, Nagata Y, Tsuda M
    • Total Pages
      279-291
    • Publisher
      Springer Verlag, Tokyo
  • [Remarks]

    • URL

      http://www.ige.tohoku.ac.jp/joho/gf/index.php

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Published: 2015-06-25  

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