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Comparative genome analysis of parthenogenetic nematode

Research Project

Project/Area Number 25250025
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Genome biology
Research InstitutionNational Institute of Genetics

Principal Investigator

KOHARA Yuji  国立遺伝学研究所, 系統生物研究センター, 特任教授 (70135292)

Project Period (FY) 2013-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥45,370,000 (Direct Cost: ¥34,900,000、Indirect Cost: ¥10,470,000)
Fiscal Year 2016: ¥8,970,000 (Direct Cost: ¥6,900,000、Indirect Cost: ¥2,070,000)
Fiscal Year 2015: ¥9,880,000 (Direct Cost: ¥7,600,000、Indirect Cost: ¥2,280,000)
Fiscal Year 2014: ¥11,700,000 (Direct Cost: ¥9,000,000、Indirect Cost: ¥2,700,000)
Fiscal Year 2013: ¥14,820,000 (Direct Cost: ¥11,400,000、Indirect Cost: ¥3,420,000)
Keywordsゲノムアセンブリ / 線虫 / 単為生殖 / 進化 / 減数分裂 / ゲノム多様性 / 単為発生 / 染色体 / 遺伝子 / 発生・分化
Outline of Final Research Achievements

Although sexual reproduction is prevailing among eukaryotes, the nematode Diploscapter coronatus, a close relative of the model C. elegans, reproduces parthenogenetically. Neither males nor sperm have been observed and some steps of meiosis are apparently skipped in this species. To uncover the genomic changes associated with parthenogenetic reproduction, we carried out a genome analysis and we found that nearly 90% of the 170 Mbp draft genome sequences constitute homologous pairs with a 5.7% heterozygosity on average, meaning that the 170 Mbp sequences correspond to the diploid genome. Fluorescent staining showed that the D. coronatus genome consists of two chromosomes (2n = 2). Although 59 % of the C. elegans genes were found in the genome, many genes including those involved in sex determination and meiosis were missing or very divergent. Among them the defect of meiotic kleisins (rec-8 and coh-3/4) may be related to parthenogenetic reproduction.

Report

(5 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (14 results)

All 2016 2015 2014 2013 Other

All Int'l Joint Research (2 results) Journal Article (2 results) (of which Peer Reviewed: 2 results,  Open Access: 2 results) Presentation (7 results) (of which Int'l Joint Research: 1 results,  Invited: 1 results) Remarks (3 results)

  • [Int'l Joint Research] ケルン大学(ドイツ)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] ケルン大学(ドイツ)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] A whole-mount in situ hybridization method for microRNA detection in Caenorhabditis elegans.2016

    • Author(s)
      Andachi Y. and Kohara Y.
    • Journal Title

      RNA

      Volume: 22(7) Issue: 7 Pages: 1099-106

    • DOI

      10.1261/rna.054239.115

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Co-expression of the transcription factors CEH-14 and TTX-1 regulates AFD neuron-specific genes gcy-8 and gcy-18 in C. elegans.2015

    • Author(s)
      Kagoshima H, and Kohara Y.
    • Journal Title

      Dev Biol.

      Volume: 15 Issue: 2 Pages: 325-336

    • DOI

      10.1016/j.ydbio.2015.01.010

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] C.elegans初期胚における母性mex-3 mRNAの局在化は細胞運命の確実な決定に必要である2016

    • Author(s)
      金野宏之、野口浩毅、小原雄治
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] C.elegans初期胚における母性mex-3 mRNAの局在化は細胞運命の決定に必要である。2015

    • Author(s)
      金野宏之、野口浩毅、小原雄治
    • Organizer
      38回日本分子生物学会年会・第88回日本生化学大会合同大会
    • Place of Presentation
      神戸
    • Year and Date
      2015-12-03
    • Related Report
      2015 Annual Research Report
  • [Presentation] Mechanism and significance of the maternal mex-3 mRNA localization in C. elegans.2015

    • Author(s)
      Hiroyuki Konno, Koki Noguchi, Yuji Kohara
    • Organizer
      20th International C. elegans Meeting
    • Place of Presentation
      UCLA, USA
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Genome and transcriptome analysis of the parthenogenetic nematode Diploscapter coronatus2014

    • Author(s)
      Hideaki Hiraki, Hiroshi Kagoshima, Yumiko Ueta, Christopher Kraus, Philipp Schiffer, Einhard Schierenberg and Yuji Kohara
    • Organizer
      日本分子生物学会第37回年会
    • Place of Presentation
      横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] Mechanisms and implication of the maternal mex-3 mRNA localization in C. elegans.2014

    • Author(s)
      Hiroyuki Konno, Koki Noguchi and Yuji Kohara
    • Organizer
      日本分子生物学会第37回年会
    • Place of Presentation
      横浜
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] The worm transcriptome: the past and the future2014

    • Author(s)
      Yuji Kohara
    • Organizer
      C. elegans Development Topic Meeting / Asia-Pacific C. elegans Meeting
    • Place of Presentation
      Nara
    • Year and Date
      2014-07-16 – 2014-07-19
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Genome and transcriptome analysis of the parthenogenetic nematode Diploscapter coronatus2013

    • Author(s)
      H. Hiraki, H. Kagoshima, Y. Ueta, C. Kraus, P. Schiffer, E. Schierenberg, Y. Kohara
    • Organizer
      日本分子生物学会第36回年会
    • Place of Presentation
      神戸ポートアイランド
    • Related Report
      2013 Annual Research Report
  • [Remarks] D.coronatusゲノムブラウザ

    • URL

      http://nematode.lab.nig.ac.jp/d_coronatus/

    • Related Report
      2016 Annual Research Report
  • [Remarks] 線虫遺伝子発現データベース(NEXTDB)

    • URL

      http://nematode.lab.nig.ac.jp/

    • Related Report
      2016 Annual Research Report 2015 Annual Research Report 2014 Annual Research Report
  • [Remarks] 線虫遺伝子発現データベース(NEXTDB)

    • URL

      http://nematode.lab.nig.ac.jp/

    • Related Report
      2013 Annual Research Report

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Published: 2013-05-15   Modified: 2019-07-29  

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