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Generation of a high-resolution genome map using haploid and hybrid organisms and its application to genetic analysis

Research Project

Project/Area Number 20H00429
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Review Section Medium-sized Section 40:Forestry and forest products science, applied aquatic science, and related fields
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(農学部), 教授 (30231872)

Co-Investigator(Kenkyū-buntansha) 黒河内 寛之  東京大学, 大学院農学生命科学研究科(農学部), 助教 (00609000)
稲野 俊直  近畿大学, 水産研究所, 准教授 (50604609)
川村 猛  東京大学, アイソトープ総合センター, 准教授 (70306835)
Project Period (FY) 2020-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥45,500,000 (Direct Cost: ¥35,000,000、Indirect Cost: ¥10,500,000)
Fiscal Year 2022: ¥8,710,000 (Direct Cost: ¥6,700,000、Indirect Cost: ¥2,010,000)
Fiscal Year 2021: ¥8,710,000 (Direct Cost: ¥6,700,000、Indirect Cost: ¥2,010,000)
Fiscal Year 2020: ¥19,370,000 (Direct Cost: ¥14,900,000、Indirect Cost: ¥4,470,000)
Keywordsハプロイド連鎖解析法 / ハイブリッド連鎖解析法 / アユ / ニホンウナギ / トゲウオ / クロマグロ / チョウザメ / マツタケ / ハイブリッドゲノムシーケンシング / ハプロイドゲノムシーケンシング / アユ半数体 / チョウザメ・ヘラチョウザメ / ナマズ・ギギ / マツタケゲノム解読 / シイタケゲノム / 全ゲノムSNPタイピング / ハプロイド / ハイブリッド / 連鎖解析 / ゲノム解析 / 非モデル生物 / 連鎖地図 / SNPタイピング / ハイブリッド個体 / 雑種個体 / 半数体 / エクソソーム / ダブルハプロイド / ハプロイドシーケンシング / ハイブリッドシーケンシング / クロマグロ×スマ / ニホンウナギ×マアナゴ / ニホンウナギ×オオウナギ / ブリ×ヒラマサ / 食用性キノコ / 雌性発生・単為発生 / 超高精度連鎖地図 / SELDLA / ゲノムアセンブル
Outline of Research at the Start

申請者らは雑種個体やハプロイド個体等を利用して、高分解能の連鎖地図を作製する手法を確立し、そのための専用のソフトSELDLAを開発した。本研究では魚介類、樹木、菌類、哺乳類などでその手法を応用する。雑種生物の作製に加え、自然界の雑種のサンプリング、花粉由来カルスや一核菌糸の作製、哺乳類雑種胚盤胞の作製などの試みを行う。雑種作製のアクセプターとなるマスター種を定める。シーケンシングに関してBAC作製の技術を活用する。高精度ドラフトゲノムを構築し、魚類、樹木、菌類の種分化メカニズム、魚性決定遺伝子の同定、樹木・菌間組合せのメカニズム解明、有用遺伝子の探索とゲノム育種、ゲノミックセレクションに取り組む。

Outline of Final Research Achievements

We generated haploid and hybrid experimental materials, and performed their DNA typing, linkage mapping and contig/scaffold alignment with SELDRA, then generated genome draft sequences, and genome completion sequencing. Generations of hybrid of Japanese eel and common Japanese conger eel, etc., were conducted, and haploid and double haploid individuals of catfish and various sturgeon were generated, and haploid individuals of Ayu were generated. Androgensis of the Japanese two color carp was also performed. Complete genome sequence, T2T of matsutake mushroom was conducted. Linkage maps of Kawakawa (Euthynnus affinis) and Pacific bluefin tuna were generated by hybrid method. We attempted to expand to haploid typing using sperm and conducted it in stickleback. Sequences for typing were obtained for other hybrid and haploid individuals.

Academic Significance and Societal Importance of the Research Achievements

ゲノム情報は生物学にとって最も重要な基盤の一つである。2005年に出現した次世代シーケンサは、あらゆる生物のゲノム解析を容易にしたが、ゲノムシーケンスを染色体レベルにまで構築するのは未だ容易ではない。我々は染色体レベルにゲノムシーケンスを整列化させる効率的な2つの方法を確立し、その有用性を実証した。これらの手法はHi-C法等とともに、あらゆる真核生物のゲノム解析にとって有用な手法であり、高品質のゲノム配列の構築に貢献できる。得られる高品質ゲノム配列の有用性は基礎的な生物学の諸分野だけでなく、農林水産学などの応用分野においても極めて高く、今後、基礎的な学術分野や諸応用分野への貢献が期待できる。

Report

(5 results)
  • 2023 Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • 2020 Comments on the Screening Results   Annual Research Report
  • Research Products

    (13 results)

All 2023 2022 2021 2020 Other

All Journal Article (11 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 10 results,  Open Access: 10 results) Presentation (1 results) (of which Int'l Joint Research: 1 results) Remarks (1 results)

  • [Journal Article] Synthesis and cloning of long repeat sequences using single-stranded circular DNA2023

    • Author(s)
      Bhuiyan Afsana、Asakawa Shuichi
    • Journal Title

      Frontiers in Bioengineering and Biotechnology

      Volume: 11

    • DOI

      10.3389/fbioe.2023.1115159

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Draft genome sequencing and assembly of Risso's dolphin, <i>Grampus griseus</i>2023

    • Author(s)
      Senevirathna Jayan D.M.、Yonezawa Ryo、Saka Taiki、Hiramatsu Yuka、Smith Ashley Rinka、Igarashi Yoji、Yoshitake Kazutoshi、Kinoshita Shigeharu、Funasaka Noriko、Asakawa Shuichi
    • Journal Title

      Journal of Genomics

      Volume: 11 Pages: 9-13

    • DOI

      10.7150/jgen.78761

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Telomere-to-telomere genome assembly of matsutake (<i>Tricholoma matsutake</i>)2022

    • Author(s)
      Kurokochi Hiroyuki、Tajima Naoyuki、Sato Mitsuhiko P.、Yoshitake Kazutoshi、Asakawa Shuichi、Isobe Sachiko、Shirasawa Kenta
    • Journal Title

      biorxiv

      Volume: 2022.07.25

    • DOI

      10.1101/2022.07.25.501483

    • Related Report
      2022 Annual Research Report
  • [Journal Article] Construction of a chromosome-level Japanese stickleback species genome using ultra-dense linkage analysis with single-cell sperm sequencing2022

    • Author(s)
      Yoshitake Kazutoshi、Ishikawa Asano、Yonezawa Ryo、Kinoshita Shigeharu、Kitano Jun、Asakawa Shuichi
    • Journal Title

      NAR Genomics and Bioinformatics

      Volume: 4 Issue: 2

    • DOI

      10.1093/nargab/lqac026

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Selection of a reference gene for studies on lipid‐related aquatic adaptations of toothed whales ( <i>Grampus griseus</i> )2021

    • Author(s)
      Senevirathna Jayan D. M.、Yonezawa Ryo、Saka Taiki、Igarashi Yoji、Funasaka Noriko、Yoshitake Kazutoshi、Kinoshita Shigeharu、Asakawa Shuichi
    • Journal Title

      Ecology and Evolution

      Volume: 11 Issue: 23 Pages: 17142-17159

    • DOI

      10.1002/ece3.8354

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A Review of Discovery Profiling of PIWI-Interacting RNAs and Their Diverse Functions in Metazoans2021

    • Author(s)
      Huang Songqian、Yoshitake Kazutoshi、Asakawa Shuichi
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 22 Issue: 20 Pages: 11166-11166

    • DOI

      10.3390/ijms222011166

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Chromosome-Scale Genome Assembly and Transcriptome Assembly of Kawakawa Euthynnus affinis; A Tuna-Like Species2021

    • Author(s)
      Havelka Milo、Sawayama Eitaro、Saito Taiju、Yoshitake Kazutoshi、Saka Daiki、Ineno Toshinao、Asakawa Shuichi、Takagi Motohiro、Goto Rie、Matsubara Takahiro
    • Journal Title

      Frontiers in Genetics

      Volume: 12 Pages: 739781-739781

    • DOI

      10.3389/fgene.2021.739781

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Another polymorphic mitochondrial genome of <i>Grampus griseus</i> and phylogeny of family Delphinidae2021

    • Author(s)
      Senevirathna Jayan Duminda M.、Yonezawa Ryo、Saka Taiki、Igarashi Yoji、Yoshitake Kazutoshi、Kinoshita Shigeharu、Funasaka Noriko、Asakawa Shuichi
    • Journal Title

      Mitochondrial DNA Part B

      Volume: 6 Issue: 9 Pages: 2569-2571

    • DOI

      10.1080/23802359.2021.1959453

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Multi-Omics Approaches and Radiation on Lipid Metabolism in Toothed Whales2021

    • Author(s)
      Senevirathna Jayan D. M.、Asakawa Shuichi
    • Journal Title

      Life

      Volume: 11 Issue: 4 Pages: 364-364

    • DOI

      10.3390/life11040364

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach2021

    • Author(s)
      Huang Songqian、Yoshitake Kazutoshi、Asaduzzaman Md、Kinoshita Shigeharu、Watabe Shugo、Asakawa Shuichi
    • Journal Title

      RNA Biology

      Volume: - Issue: 11 Pages: 1-14

    • DOI

      10.1080/15476286.2020.1867798

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Characterization and phylogenetic position of two sympatric sister species of toxic flatworms Planocera multitentaculata and Planocera reticulata (Platyhelminthes: Acotylea)2020

    • Author(s)
      Ryo Yonezawa, Shiro Itoi, Yoji Igarashi, Kazutoshi Yoshitake, Hikaru Oyama, Shigeharu Kinoshita, Rei Suo, Shinichi Yokobori, Haruo Sugita, Shuichi Asakawa
    • Journal Title

      Mitochondrial DNA Part B

      Volume: 未定 Issue: 3 Pages: 2352-2354

    • DOI

      10.1080/23802359.2020.1730255

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Localization of KK13 peptide and their potential against ALS2022

    • Author(s)
      Afsana Bhuiyan・Shuichi Asakawa ・Nahoko Bailey Kobayashi ・Tetsuhiko Yoshida
    • Organizer
      American Society of Human Genetics Annual Meeting
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Remarks] マツタケのゲノムを完全解読 ~ 希少化するマツタケの保全に向けて ~

    • URL

      https://www.a.u-tokyo.ac.jp/topics/topics_20230508-1.html

    • Related Report
      2022 Annual Research Report

URL: 

Published: 2020-04-28   Modified: 2025-01-30  

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