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High quality genome assembly and construction of high-resolution linkage map by sequencing and SNPs typing of haploid genome individuals

Research Project

Project/Area Number 25640099
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Genome biology
Research InstitutionThe University of Tokyo

Principal Investigator

ASAKAWA Shuichi  東京大学, 大学院農学生命科学研究科, 教授 (30231872)

Project Period (FY) 2013-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2014: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2013: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywordsゲノムシーケンシング / トラフグ / ニジマス / ブリ / 雌性発生 / ダブルハプロイド / ハプロイド / ホモ接合 / ダブルハプロイド/ハプロイド / 第一卵割阻止 / ハプロイドゲノム / 連鎖地図
Outline of Final Research Achievements

In this study, we planed to prepare individuals of double haploid / haploid using the techniques of gynogenesis in fish, and then we examined the usability of it for the genome sequencing, and construction of the linkage map produced by the SNP typing.
Genome sequencing results show that the N50 contig and scaffold from the double haploid individuals are much longer than those from normal hetero diploid individuals. These results indicate the effectiveness of the use of double-haploid/haploid individuals for de novo sequencing of diploid organisms.

Report

(3 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • Research Products

    (5 results)

All 2015 2014 2013

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Acknowledgement Compliant: 2 results,  Open Access: 1 results) Presentation (3 results) (of which Invited: 1 results)

  • [Journal Article] Characterization of the torafugu (Takifugu rubripes) immunoglobulin heavy chain gene locus.2015

    • Author(s)
      Fu X, Zhang H, Tan E, Watabe S, Asakawa S.
    • Journal Title

      Immunogenetics.

      Volume: 67(3) Issue: 3 Pages: 179-93

    • DOI

      10.1007/s00251-014-0824-z

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Dramatic improvement in genome assembly achieved using doubled-haploid genomes.2014

    • Author(s)
      Zhang H, Tan E, Suzuki Y, Hirose Y, Kinoshita S, Okano H, Kudoh J, Shimizu A, Saito K, Watabe S, Asakawa S.
    • Journal Title

      Sci Rep.

      Volume: 4 Issue: 1 Pages: 6780-6780

    • DOI

      10.1038/srep06780

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Utilization of a doubled-haploid individual in construction of a high-quality torafugu (Takifugu rubripes) genome assembly2013

    • Author(s)
      Hong Zhang, Shigeharu Kinoshita, Engkong Tan, Yutaka Suzuki, Atsushi Shimizu, Hideyuki Okano, Jun Kudoh, Kazuyoshi Saito, Shugo Watabe, Shuichi Asakawa
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸
    • Related Report
      2013 Research-status Report
  • [Presentation] ダブルハプロイド個体を活用した高品質トラフグゲノムアセンブリの作成2013

    • Author(s)
      張虹、陳盈光、木下滋晴、浅川修一、鈴木穣、清水厚志、岡野栄之、工藤 純、斎藤和敬、渡部終五
    • Organizer
      平成25年度日本水産学会秋季大会
    • Place of Presentation
      津
    • Related Report
      2013 Research-status Report
  • [Presentation] Genome and transcriptome analysis of aquatic organisms by next generation sequencing2013

    • Author(s)
      S. Asakawa
    • Organizer
      FABA2013
    • Place of Presentation
      Erzurum, Turkey
    • Related Report
      2013 Research-status Report
    • Invited

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Published: 2014-07-25   Modified: 2019-07-29  

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