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Population genetic theory and comparative genomics to understand the evolutionary mechanism in noncoding DNA

Planned Research

Project AreaFunctions of non-coding DNA region for genome integrity
Project/Area Number 23114004
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 InstitutionThe Graduate University for Advanced Studies

Principal Investigator

Innan Hideki  総合研究大学院大学, その他の研究科, 准教授 (90444140)

Project Period (FY) 2011-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥78,910,000 (Direct Cost: ¥60,700,000、Indirect Cost: ¥18,210,000)
Fiscal Year 2015: ¥13,910,000 (Direct Cost: ¥10,700,000、Indirect Cost: ¥3,210,000)
Fiscal Year 2014: ¥13,910,000 (Direct Cost: ¥10,700,000、Indirect Cost: ¥3,210,000)
Fiscal Year 2013: ¥14,690,000 (Direct Cost: ¥11,300,000、Indirect Cost: ¥3,390,000)
Fiscal Year 2012: ¥14,430,000 (Direct Cost: ¥11,100,000、Indirect Cost: ¥3,330,000)
Fiscal Year 2011: ¥21,970,000 (Direct Cost: ¥16,900,000、Indirect Cost: ¥5,070,000)
Keywords集団遺伝 / ゲノム進化 / 非コード領域 / 進化 / ゲノム
Outline of Final Research Achievements

This research project was aimed to understand the evolutionary mechanisms in noncoding DNA regions, which constitute the majority of the eukaryote genomes. We have carried out theoretical works on population genetics and molecular evolution specifically for noncoding regions, where mutational mechanisms are generally more complex than coding regions. The theory was applied to genomic data from various species including Schizosaccharomyces pombe, rice, human, Arabidopsis thaliana. We found that various modes of natural selection has shaped the current pattern of genome variation within and between species. It was also found that there are a number of noncoding regions that are under strong purifying selection, indicating crucial roles of noncoding regions.

Report

(6 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (19 results)

All 2015 2014 2013 2012 2011

All Journal Article (18 results) (of which Peer Reviewed: 15 results,  Acknowledgement Compliant: 1 results,  Open Access: 3 results) Book (1 results)

  • [Journal Article] Evaluating the performance of neutrality tests of a local community using a niche-structured simulation model.2015

    • Author(s)
      Takeuchi, Y., and H. Innan
    • Journal Title

      Oikos

      Volume: 124 Issue: 9 Pages: 1203-1214

    • DOI

      10.1111/oik.01703

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Spreading good news2015

    • Author(s)
      Fawcett, J. A., and H. Innan
    • Journal Title

      eLife

      Volume: 4

    • DOI

      10.7554/elife.05899

    • Related Report
      2015 Annual Research Report
    • Open Access
  • [Journal Article] Spreading good news2015

    • Author(s)
      Jeffrey A. Fawcett, Hideki Innan
    • Journal Title

      eLife

      Volume: 4

    • DOI

      10.7554/elife.07108

    • Related Report
      2014 Annual Research Report
    • Open Access
  • [Journal Article] Population genomics of the fission yeast Schizosaccharomyces pombe2014

    • Author(s)
      Jeffrey A. Fawcett, Tetsushi Iida, Shohei Takuno, Ryuichi P. Sugino, Tomoyuki Kado, Kazuto Kugou, Sachiko Mura, Takehiko Kobayashi, Kunihiro Ohta, Jun-ichi Nakayama, Hideki Innan
    • Journal Title

      PLOS ONE

      Volume: 9 Issue: 8 Pages: e104241-e104241

    • DOI

      10.1371/journal.pone.0104241

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Divergent selection for opsin gene variation in guppy (Poecilia reticulata) populations of Trinidad and Tobago2014

    • Author(s)
      Tezuka, A., Kasagi, S., van Oosterhout, C., McMullan, M., Iwasaki, W. M., Kasai,D., Yamamichi, M., Innan, H., Kawamura, S. and Kawata, M.
    • Journal Title

      Heredity

      Volume: (Published Online) Issue: 5 Pages: 381-389

    • DOI

      10.1038/hdy.2014.35

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Meiotic recombination cold spots in chromosomal cohesion sites2014

    • Author(s)
      Masaru Ito, Kazuto Kugou, Jeffrey A. Fawcett, Sachiko Mura, Sho Ikeda, Hideki Innan, Kunihiro Ohta
    • Journal Title

      Genes to Cells

      Volume: (Published online) Issue: 5 Pages: 359-378

    • DOI

      10.1111/gtc.12138

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The linkage method, a novel approach for SNP detection and haplotype reconstruction from a single diploid individual with next generation sequence data2013

    • Author(s)
      Sasaki, E., Sugino, R. P., and H. Innan
    • Journal Title

      Mol. Biol. Evol.

      Volume: 30 Issue: 9 Pages: 2187-2196

    • DOI

      10.1093/molbev/mst103

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Competition between the sperm of a single male can increase the evolutionary rate of haploid expressed genes2013

    • Author(s)
      Ezawa, K., and H. Innan
    • Journal Title

      Genetics

      Volume: 194 Issue: 3 Pages: 709-719

    • DOI

      10.1534/genetics.113.152066

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Population genetics and molecular evolution of DNA sequences in Transposable elements. I. A simulation framework2013

    • Author(s)
      Kijima, TE, and H. Innan
    • Journal Title

      Genetics

      Volume: 195 Issue: 3 Pages: 957-967

    • DOI

      10.1534/genetics.113.150292

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The role of gene conversion in preservation of rearrangement hotspots in the human genome.2013

    • Author(s)
      Fawcett, J. A., and H. Innan
    • Journal Title

      Trends in Genetics

      Volume: 29 Issue: 10 Pages: 561-568

    • DOI

      10.1016/j.tig.2013.07.002

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Natural selection on gene order in the genome re-organization process after whole genome duplication of yeast2012

    • Author(s)
      Sugino, R. P., and H. Innan
    • Journal Title

      Mol. Biol. Evol.

      Volume: 29 Issue: 1 Pages: 71-79

    • DOI

      10.1093/molbev/msr118

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees2012

    • Author(s)
      山道真人、五條堀淳、印南秀樹
    • Journal Title

      Molecular Biology and Evolution

      Volume: 29巻 Issue: 1 Pages: 145-156

    • DOI

      10.1093/molbev/msr172

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Population genomics in Bacteria: A case study of Staphylococcus aureus2012

    • Author(s)
      Takuno, S., Kado, T., Sugino, R. P., Nakhleh, and H. Innan
    • Journal Title

      Mol. Biol. Evol.

      Volume: 29 Issue: 2 Pages: 797-809

    • DOI

      10.1093/molbev/msr249

    • Related Report
      2012 Annual Research Report
  • [Journal Article] The coalescent with selection on copy number variants2012

    • Author(s)
      KM. Teshima, H.Innan
    • Journal Title

      Genetics

      Volume: 190 Issue: 3 Pages: 1077-1086

    • DOI

      10.1534/genetics.111.135343

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Modeling evolutionary growth of a microRNA-mediated regulation system2012

    • Author(s)
      Akita Tetsuya, Takuno Shohei, Tnngn Hirloki
    • Journal Title

      Journal of Theoretical Biology

      Volume: 311 Pages: 54-65

    • DOI

      10.1016/j.jtbi.2012.07.011

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Neutral and non-neutral evolution of duplicated genes with gene conversion2011

    • Author(s)
      Fawcett, J. A.
    • Journal Title

      Genes

      Volume: 2 Issue: 1 Pages: 191-209

    • DOI

      10.3390/genes2010191

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The rate and tract length of gene conversion between duplicated genes2011

    • Author(s)
      Mansai, S. P.
    • Journal Title

      Genes

      Volume: 2 Issue: 2 Pages: 313-331

    • DOI

      10.3390/genes2020313

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Selection fine tunes the expression of microRNA target genes in Arabidopsis thaliana.2011

    • Author(s)
      Takuno, S.
    • Journal Title

      Mol. Biol. Evol.

      Volume: 28 Issue: 9 Pages: 2429-2434

    • DOI

      10.1093/molbev/msr084

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Book] ゲノム進化メカニズムと情報学的解析2015

    • Author(s)
      岩嵜航、印南秀樹
    • Total Pages
      12
    • Publisher
      化学同人
    • Related Report
      2015 Annual Research Report

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Published: 2011-08-01   Modified: 2019-07-29  

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