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Study of the occurrence of mutations and adaptive genome evolution via genomic analyses

Planned Research

Project AreaSystematic study of chromosome adaptation
Project/Area Number 22125009
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionHokkaido University

Principal Investigator

WATANABE Hidemi  北海道大学, 情報科学研究科, 教授 (30322754)

Co-Investigator(Kenkyū-buntansha) KOYANAGI Kanako  北海道大学, 大学院情報科学研究科, 准教授 (20362840)
Project Period (FY) 2010-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥79,300,000 (Direct Cost: ¥61,000,000、Indirect Cost: ¥18,300,000)
Fiscal Year 2014: ¥14,690,000 (Direct Cost: ¥11,300,000、Indirect Cost: ¥3,390,000)
Fiscal Year 2013: ¥15,470,000 (Direct Cost: ¥11,900,000、Indirect Cost: ¥3,570,000)
Fiscal Year 2012: ¥16,380,000 (Direct Cost: ¥12,600,000、Indirect Cost: ¥3,780,000)
Fiscal Year 2011: ¥16,120,000 (Direct Cost: ¥12,400,000、Indirect Cost: ¥3,720,000)
Fiscal Year 2010: ¥16,640,000 (Direct Cost: ¥12,800,000、Indirect Cost: ¥3,840,000)
Keywords突然変異 / 組換え / 修復 / ゲノム / 進化 / 自然選択 / ヒトアデノウイルス / 酵母 / 相同組換え / DNA二重鎖切断 / 二本鎖DNA切断修復 / 非相同末端結合 / アデノウイルス / 突然変異率 / 適応進化 / 比較解析 / 正の自然選択 / 継代培養
Outline of Final Research Achievements

In order to obtain the fundamental properties of occurrence of genomic mutations so as to identify genomic changes that have led to adaptive evolution, i.e., genome adaptation, via finding significant deviations from the expectations calculated with the properties of the occurrence of mutations, we artificially introduced random double-strand breaks (DSBs) to the budding yeast genome and detected occurred mutations during repair of the DSBs by sequencing the whole genomes. In addition, we have computationally traced back genomic changes of natural human adenoviruses (HAdV), and it was suggested that HAdVs have changed via homologous recombination events between distant relatives. The statistical properties of this type of changes in HAdV indicate that the recombinant forms have been selected for adaptation.

Report

(6 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (29 results)

All 2015 2014 2013 2012 2011 2010

All Journal Article (11 results) (of which Peer Reviewed: 11 results,  Acknowledgement Compliant: 3 results,  Open Access: 1 results) Presentation (18 results) (of which Invited: 4 results)

  • [Journal Article] Interregional coevolution analysis revealing functional/structural interrelatedness between different genomic regions in Human mastadenovirus D2015

    • Author(s)
      Gabriel Gonzalez, Kanako Ono Koyanagi, Koki Aoki, Hidemi Watanabe
    • Journal Title

      Journal of Virology

      Volume: 89 Issue: 12 Pages: 6209-6217

    • DOI

      10.1128/jvi.00515-15

    • NAID

      120005672366

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Intertypic modular exchanges of genomic segments by homologous recombination at universally conserved segments in human adenovirus species D2014

    • Author(s)
      Gabriel Gonzalez, Kanako O. Koyanagi, Koki Aoki, Nobuyoshi Kitaichi, Shigeaki Ohno, Hisatoshi Kaneko,d, Susumu Ishida, Hidemi Watanabe
    • Journal Title

      Gene

      Volume: 547 Issue: 1 Pages: 10-17

    • DOI

      10.1016/j.gene.2014.04.018

    • Related Report
      2014 Annual Research Report 2013 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] A Novel Complex Recombinant Form of Type 48-Related Human Adenovirus Species D Isolated in Japan2014

    • Author(s)
      Tsuguto Fujimoto, Shotaro Yamane, Tomoko Ogawa, Nozomu Hanaoka, Atsushi Ogura, Chiemi Hotta, Takeshi Niwa, Yakou Chiba, Gabriel Gonzalez, Koki Aoki, Kanako Ono Koyanagi, Hidemi Watanabe
    • Journal Title

      Japanese Journal of Infectious Diseases

      Volume: 67 Issue: 4 Pages: 282-287

    • DOI

      10.7883/yoken.67.282

    • NAID

      130004757096

    • ISSN
      1344-6304, 1884-2836
    • Related Report
      2014 Annual Research Report 2013 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Bioinformatics on new human adenoviruses causing nosocomial infection2013

    • Author(s)
      Koki Aoki, Hisatosi Kaneko, Nobuyoshi Kitaichi, Hidemi Watanabe,Susumu Ishida, Shigeaki Ohno
    • Journal Title

      Nippon Ganka Gakkai Zasshi

      Volume: 117 Pages: 721-726

    • NAID

      10031194625

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification of contamination in the American Type Culture Collection stock of human adenovirus type 8 by whole genome sequencing.2013

    • Author(s)
      Yamane S, Lee A, Hanaoka N, Gonzalez G, Kaneko H, Ishida S, Kitaichi N, Ohno S, Koyanagi K, Aoki K, Fujimoto T, Yawata N, Watanabe H.
    • Journal Title

      J Virol

      Volume: 87 Issue: 2 Pages: 1285-1286

    • DOI

      10.1128/jvi.02875-12

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evolutionary force of AT-rich repeats to trap genomic and episomal DNAs in the rice genome: lessons from endogenous pararetrovirus.2012

    • Author(s)
      Liu, R.
    • Journal Title

      The Plant Journal

      Volume: 72 Issue: 5 Pages: 817-828

    • DOI

      10.1111/tpj.12002

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comparative genome analysis of three eukaryotic parasites with differing abilities of leukocyte transformation reveals key mediators of Theileria-induced leukocyte-transformation.2012

    • Author(s)
      Kyoko Hayashida*, Yuichiro Hara*, Takashi Abe*, et al. (*equal contribution).
    • Journal Title

      mBio

      Volume: 3 Issue: 5

    • DOI

      10.1128/mbio.00204-12

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] In silico and in vivo identification of the intermediate filament vimentin that is downregulated downstream of Brachyury during Xenopus embryogenesis2012

    • Author(s)
      Atsuko Yamada, Kanako O.Koyanagi, Hidemi Watanabe
    • Journal Title

      Gene

      Volume: 491 Issue: 2 Pages: 232-236

    • DOI

      10.1016/j.gene.2011.09.007

    • NAID

      120003762597

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Recombination analysis of intermediate human adenovirus type 53 in Japan by complete genome sequence2011

    • Author(s)
      Hisatoshi Kaneko, Koki Aoki, Susumu Ishida, Shigeaki Ohno, Nobuyoshi Kitaichi, Hiroaki Ishiko, Tsuguto Fujimoto, Yoshifumi Ikeda, Masako Nakamura, Gabriel Gonzalez, Kanako O.Koyanagi, Hidemi Watanabe, Tatsuo Suzutani
    • Journal Title

      Journal of General Virology

      Volume: 92 Issue: 6 Pages: 1251-1259

    • DOI

      10.1099/vir.0.030361-0

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Recombinant analysis of intermediate human adenovirus type 53 in Japan by complete genome sequence2011

    • Author(s)
      Hisatoshi Kaneko1, Koki Aoki, Susumu Ishida, Shigeaki Ohno, Nobuyoshi Kitaichi, Hiroaki Ishiko, Tsuguto Fujimoto, Yoshifumi Ikeda, Masako Nakamura, Gabriel Gonzalez, Kaneko O.Koyanagi, Hidemi Watanabe, Tatsuo Suzutani
    • Journal Title

      Journal of General Virology

      Volume: 92 Pages: 1251-1259

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Complete genome analysis of a novel intertypic recombinant human adenovirus causing epidemic keratoconjunctivitis in Japan2011

    • Author(s)
      Hisatoshi Kaneko, Koki Aoki, Shigeaki Ohno, Hiroaki Ishiko, Tsuguto Fujimoto, Masayuki Kikuchi, Seiya Harada, Gabriel Gonzalez, Kanako O Koyanagi, Hidemi Watanabe, Tatsuo Suzutani
    • Journal Title

      Journal of Clinical Microbiology

      Volume: 49 Pages: 484-490

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] Recombination hotspots enabling intertypic modular exchanges in human adenovirus species D2014

    • Author(s)
      G Gonzalez, KO Koyanagi, K Aoki, N Kitaichi, S Ohno, H Kaneko, S Ishida, H Watanabe
    • Organizer
      The 11th International Adenovirus Meeting
    • Place of Presentation
      UC San Diego, San Diego, USA
    • Year and Date
      2014-07-18
    • Related Report
      2014 Annual Research Report
  • [Presentation] New subtypes of human adenovirus 8 from Europe2014

    • Author(s)
      Laura Panto, Gabriel Gonzalez, Shotaro Yamane, Gabor Reuter, Peter Pankovics, Balazs Harrach, Goran Wadell, Koki Aoki, Kanako O. Koyanagi and Hidemi Watanabe
    • Organizer
      The 11th International Adenovirus Meeting
    • Place of Presentation
      UC San Diego, San Diego, USA
    • Year and Date
      2014-07-18
    • Related Report
      2014 Annual Research Report
  • [Presentation] Evolutionary origins of human adenovirus types 8 and 542014

    • Author(s)
      Shotaro Yamane, Gabriel Gonzalez, Laura Panto, Yuichiro Okuyama, Nobuyoshi Kitaichi, Hisatoshi Kaneko, Y. Jerold Gordon, Nobuyo Yawata, Kanako O. Koyanagi, Koki Aoki and Hidemi Watanabe
    • Organizer
      The 11th International Adenovirus Meeting
    • Place of Presentation
      UC San Diego, San Diego, USA
    • Year and Date
      2014-07-18
    • Related Report
      2014 Annual Research Report
  • [Presentation] Adenoviral evolution in progress: new viruses in the doorstep2013

    • Author(s)
      Laura Panto, Shotaro Yamane, Goran Wadell, Koki Aoki, Kanako O Koyanagi, Hidemi Watanabe
    • Organizer
      The 3rd World Congress on Virology
    • Place of Presentation
      DoubleTree by Hilton Baltimore-BWI Airport, Baltimore, MD, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] A comparative sequence analysis of human adenovirus type 8 in the world2013

    • Author(s)
      Shotaro Yamane, Laura Panto, Gabriel Gonzalez, Kanako O Koyanagi, Koki Aoki, Hidemi Watanabe
    • Organizer
      日本アデノウィルス研究会
    • Place of Presentation
      神戸ポートピアホテル(神戸市)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] From Adenoviral Infectious Cycle to Evolutionary Patterns and Genomic Constraints2013

    • Author(s)
      Gabriel Gonzalez, Kanako O Koyanagi, Hidemi Watanabe
    • Organizer
      日本アデノウィルス研究会
    • Place of Presentation
      神戸ポートピアホテル(神戸市)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Human Adenovirus Universal Typing Primers Designed by SVM Approach2013

    • Author(s)
      Gabriel Gonzalez、小柳 香奈子、青木 功喜、渡邉 日出海
    • Organizer
      日本ウイルス学会学術集会
    • Place of Presentation
      神戸国際会議場(神戸市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] 結膜炎患者の眼から分離されたアデノウイルスD種48、60、および65型(候補株)のリコンビナント型の新しいアデノウイルス2013

    • Author(s)
      藤本 嗣人、花岡 希、小倉 惇、堀田 千恵美、仁和 岳史、Gonzalez Gabriel、渡邉 日出海
    • Organizer
      日本ウイルス学会学術集会
    • Place of Presentation
      神戸国際会議場(神戸市)
    • Related Report
      2013 Annual Research Report
  • [Presentation] Adenoviral Typing Protocol Based On Highly Conserved Regions Flanking Capsid Epitopes2012

    • Author(s)
      Gabriel Gonzalez
    • Organizer
      第60回日本ウイルス学会学術集会
    • Place of Presentation
      大阪国際会議場
    • Year and Date
      2012-11-13
    • Related Report
      2012 Annual Research Report
  • [Presentation] Performance Degradation in Molecular Divergence Time Estimation with Increase in Calibrations with Asymmetric Large Uncertainty2012

    • Author(s)
      Hidemi Watanabe
    • Organizer
      International Symposium on Evolutionary Genomics
    • Place of Presentation
      National Sun Yat-sen University (台湾)
    • Year and Date
      2012-10-19
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Identification of Recombination Hotspots on Human Adenovirus Species D Genomes2012

    • Author(s)
      Gabriel Gonzalez
    • Organizer
      10th International Adenovirus Meeting
    • Place of Presentation
      Umea University (Sweden)
    • Year and Date
      2012-06-13
    • Related Report
      2012 Annual Research Report
  • [Presentation] Identification of a non-type 8 coinfection in ATCC stock of human adenovirus type 8 (HAdV-8) by partial genome sequencing-Search for recombinants in the ATCC HAdV-8 stock2012

    • Author(s)
      Shotaro Yamane
    • Organizer
      10th International Adenovirus Meeting
    • Place of Presentation
      Umea University (Sweden)
    • Year and Date
      2012-06-13
    • Related Report
      2012 Annual Research Report
  • [Presentation] Introduction of a new HAdV-8 variant, that caused epidemic keratoconjunctivitis (EKC) in Hungary2012

    • Author(s)
      Laura Panto
    • Organizer
      10th International Adenovirus Meeting
    • Place of Presentation
      Umea University (Sweden)
    • Year and Date
      2012-06-13
    • Related Report
      2012 Annual Research Report
  • [Presentation] Classification of Human Adenovirus Types by an Alternative Method2012

    • Author(s)
      Gabriel Gonzalez
    • Organizer
      10th International Adenovirus Meeting
    • Place of Presentation
      Umea University (Sweden)
    • Year and Date
      2012-06-13
    • Related Report
      2012 Annual Research Report
  • [Presentation] ゲノム比較解析を用いたアデノウイルスの型同定と進化特性解析について2012

    • Author(s)
      渡邉日出海
    • Organizer
      第13回日本アデノウイルス研究会
    • Place of Presentation
      大阪国際会議場
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Evolutionary process behind the origin of adenovinis type 19a causing Epidemic Kerato-Conjunctivitis (EKC)2011

    • Author(s)
      Gabriel Gonzalez, Koki Aoki, Kanako O Koyanagi, Nobuyoshi Kitaichi, Shigeaki Ohno, Hisatoshi Kaneko, Hiroaki Ishiko, Susumu Ishida, Hidemi Watanabe
    • Organizer
      International Union of Microbiological Societies 2011 Congress
    • Place of Presentation
      札幌コンベンションセンター204室(札幌市)
    • Year and Date
      2011-09-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] Evolutionary Origin of Human Adenovirus 542011

    • Author(s)
      Gabriel Gonzalez, Koki Aoki, Kanako O.Koyanagi, Nobuyoshi Kitaichi, Shigeaki Ohno, Hisatoshi Kaneko, Hiroaki Ishiko, Susumu Ishida, Hidemi Watanabe
    • Organizer
      The Association for Research in Vision and Ophthalmology 2011
    • Place of Presentation
      The Greater Fort Lauderdale/Broward County Convention Center (Fort Lauderdale, Florida, US)
    • Year and Date
      2011-05-03
    • Related Report
      2011 Annual Research Report
  • [Presentation] Bioinformatics analysis over recently sequenced adenoviruses strains 53, 54 and intermediate 15-29-9 causing Epidemic Kerato-Conjunctivitis outbreaks in Japan2010

    • Author(s)
      Gabriel Gonzalez, Kanako Koyanagi, Koki Aoki, Hisatoshi Kaneko, Hidemi Watanabe
    • Organizer
      Cold Spring Harbor Meeting "Infectious Disease Genomics & Global Health"
    • Place of Presentation
      Wellcome Trust Sanger Institute, Cambridge, UK
    • Year and Date
      2010-09-12
    • Related Report
      2010 Annual Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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