• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Characterizing the roles of evolutionarily 'young' genes in development

Research Project

Project/Area Number 17K07426
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Developmental biology
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

KURAKU Shigehiro  国立研究開発法人理化学研究所, 生命機能科学研究センター, チームリーダー (40391940)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2019: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2018: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2017: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywords若い遺伝子 / ゲノム情報 / 発生プログラム / 遺伝子創成 / ゲノム進化 / 「若い」遺伝子 / de novo gene / 機能的制約 / 胚発生 / 全ゲノム情報 / 遺伝子モデル / 爬虫類 / 軟骨魚類 / 系統特異的遺伝子 / 分子進化 / 発生制御遺伝子 / 発生 / 進化 / ゲノム / エピゲノム / 遺伝子発現
Outline of Final Research Achievements

Typical life science studies focus on evolutionarily 'old' genes that are conserved throughout diverse species, because analyzing homologs of already known genes has been a mainstream of studies. To overcome that bias, the present study has focused to characterize evolutionarily 'young' genes that arose relatively recently (within 100 million years) whose homolog does not exist in many other species. As a result, the original workflow designed under this purpose identified a number of candidates that have nucleotide DNA sequences characteristic of protein-coding genes, evidence of transcription, and molecular evolutionary attributes of translation.These candidates include a considerable proportion with tissue-species expression during embryogenesis, which emphasizes the involvement of 'young' genes in developmental processes that have been regarded as conservative and their importance in addressing cross-species differences in developmental regulation.

Academic Significance and Societal Importance of the Research Achievements

本課題の遂行により、特定の種だけが持つ遺伝子に新たに光を当てるとともに、その特徴づけのための解析技術基盤を築き上げることができた。種間の共通点に目が行きがちだった比較ゲノミクスに新たな流れを創ることと期待される。伝統的な実験動物以外の生物についての解析をシームレスに行うことも本課題の重点であった。そのために行った爬虫類および軟骨魚類の全ゲノム解析を一流国際誌にて報告し、複数の国際会議にて講演してきた。その一部については大手メディアにも科学記事として取り上げられ、一般社会へ発信した。また得られた配列情報は公共リソースとして世界中の研究者が利用できる状態にある。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (27 results)

All 2020 2019 2018 2017 Other

All Journal Article (9 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 8 results,  Open Access: 6 results) Presentation (17 results) (of which Int'l Joint Research: 4 results,  Invited: 9 results) Remarks (1 results)

  • [Journal Article] Nodal paralogues underlie distinct mechanisms for visceral left-right asymmetry in reptiles and mammals2020

    • Author(s)
      Kajikawa Eriko、Horo Uzuki、Ide Takahiro、Mizuno Katsutoshi、Minegishi Katsura、Hara Yuichiro、Ikawa Yayoi、Nishimura Hiromi、Uchikawa Masanori、Kiyonari Hiroshi、Kuraku Shigehiro、Hamada Hiroshi
    • Journal Title

      Nature Ecology & Evolution

      Volume: 4 Issue: 2 Pages: 261-269

    • DOI

      10.1038/s41559-019-1072-2

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Evolution of nodal and nodal‐related genes and the putative composition of the heterodimers that trigger the nodal pathway in vertebrates2019

    • Author(s)
      Opazo Juan C.、Kuraku Shigehiro、Zavala Kattina、Toloza‐Villalobos Jessica、Hoffmann Federico G.
    • Journal Title

      Evolution & Development

      Volume: 21 Issue: 4 Pages: 205-217

    • DOI

      10.1111/ede.12292

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] ゲノム情報全盛のいま使える分子系統解析のエッセンス2019

    • Author(s)
      山口 和晃、工樂 樹洋
    • Journal Title

      Comparative Endocrinology

      Volume: 45 Issue: 166 Pages: 26-31

    • DOI

      10.5983/nl2008jsce.45.26

    • NAID

      130007612211

    • ISSN
      1882-6636, 1882-6644
    • Related Report
      2019 Annual Research Report
  • [Journal Article] Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates2018

    • Author(s)
      Hara Yuichiro、Yamaguchi Kazuaki、Onimaru Koh、Kadota Mitsutaka、Koyanagi Mitsumasa、Keeley Sean D.、Tatsumi Kaori、Tanaka Kaori、Motone Fumio、Kageyama Yuka、Nozu Ryo、Adachi Noritaka、Nishimura Osamu、Nakagawa Reiko、Tanegashima Chiharu、Kiyatake Itsuki、Matsumoto Rui、Murakumo Kiyomi、Nishida Kiyonori et al.
    • Journal Title

      Nature Ecology & Evolution

      Volume: 2 Issue: 11 Pages: 1761-1771

    • DOI

      10.1038/s41559-018-0673-5

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A de novo transcriptome assembly of the zebra bullhead shark, Heterodontus zebra.2018

    • Author(s)
      Onimaru K, Tatsumi K, Shibagaki K, Kuraku S.
    • Journal Title

      Scientific Data

      Volume: 5 Issue: 1 Pages: 180197-180197

    • DOI

      10.1038/sdata.2018.197

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei.2018

    • Author(s)
      Tanegashima C, Nishimura O, Motone F, Tatsumi K, Kadota M, Kuraku S.
    • Journal Title

      Scientific Data

      Volume: 5 Issue: 1 Pages: 180200-180200

    • DOI

      10.1038/sdata.2018.200

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes2018

    • Author(s)
      Hara Y, Takeuchi M, Kageyama Y, Tatsumi K, Hibi M, Kiyonari H, Kuraku S.
    • Journal Title

      BMC Biology

      Volume: 16 Issue: 1 Pages: 40-40

    • DOI

      10.1186/s12915-018-0509-4

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications2018

    • Author(s)
      Onimaru Koh、Kuraku Shigehiro
    • Journal Title

      Briefings in Functional Genomics

      Volume: 印刷中 Issue: 5 Pages: 352-361

    • DOI

      10.1093/bfgp/ely008

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A staging table for the embryonic development of the brownbanded bamboo shark (Chiloscyllium punctatum)2018

    • Author(s)
      Onimaru Koh、Motone Fumio、Kiyatake Itsuki、Nishida Kiyonori、Kuraku Shigehiro
    • Journal Title

      Developmental Dynamics

      Volume: 247 Issue: 5 Pages: 712-723

    • DOI

      10.1002/dvdy.24623

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Diversity and evolution of vertebrate genomes2020

    • Author(s)
      工樂樹洋
    • Organizer
      The 8th Biennial RIKEN Life Science Retreat 2020
    • Related Report
      2019 Annual Research Report
  • [Presentation] Reshaping the Polyploidized Vertebrate Genomes: Case Studies on Developmental Regulators2019

    • Author(s)
      Shigehiro Kuraku
    • Organizer
      The 6th Quest for Orthologs Meeting
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Visual ecology of whale shark revealed by whole genome sequencing.2019

    • Author(s)
      Shigehiro Kuraku
    • Organizer
      5th International Whale Shark Conference
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 脊椎動物の祖先の姿を探る:ゲノム倍加ゆえの困難と光明2019

    • Author(s)
      工樂樹洋
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] サメを知らずに脊椎動物を語れるかーゲノムから視覚を探る2019

    • Author(s)
      工樂樹洋
    • Organizer
      異分野融合による次世代光生物学研究会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Unexpectedly complicated CTCF phylogeny: lessons from lamprey and shark genomics 予想外に複雑なCTCF の分子系統: 円口類と軟骨魚類のゲノム情報を基に2019

    • Author(s)
      工樂樹洋
    • Organizer
      日本進化学会第21回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 板鰓類3種のゲノム解析:「サメらしさ」に分子から迫る2019

    • Author(s)
      原雄一郎、山口和晃、野津了、小柳光正、寺北明久、喜屋武樹、西田清徳、兵藤晋、佐藤圭一、〇工樂樹洋
    • Organizer
      異分野融合による次世代光生物学研究会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 板鰓類 3種のゲノム解析:「 サメらしさ 」に分子から迫る2019

    • Author(s)
      工樂樹洋
    • Organizer
      日本水産学会春季大会
    • Related Report
      2018 Research-status Report
  • [Presentation] Elasmobranch shark genome analysis enabled by chromosome-scale scaffolding2018

    • Author(s)
      Shigehiro Kuraku
    • Organizer
      CeMEB Marine Evolution 2018
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Genomic exploration of 400 million years of elasmobranch evolution: clues for visual ecology of sharks2018

    • Author(s)
      Shigehiro Kuraku
    • Organizer
      The 1st AsiaEvo Conference
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] ゲノム情報が切り拓く分子レベルのサメ研究の現状と展望2018

    • Author(s)
      工樂樹洋
    • Organizer
      板鰓類シンポジウム2018
    • Related Report
      2018 Research-status Report
  • [Presentation] Genomic exploration of ‘fish’ diversity including jawless and cartilaginous fishes2018

    • Author(s)
      工樂樹洋
    • Organizer
      第24回小型魚類研究会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Anti-model’ biology assisted by whole genome analysis of sharks and reptiles2018

    • Author(s)
      工樂樹洋
    • Organizer
      第51回日本発生生物学会
    • Related Report
      2018 Research-status Report
  • [Presentation] Asymmetric evolution of paralogs in vertebrate genomes2017

    • Author(s)
      工樂 樹洋
    • Organizer
      Seminar for SciLifeLab at Karolinska Institute
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Elucidating the early process of vertebrate genome evolution2017

    • Author(s)
      工樂 樹洋
    • Organizer
      The Svedberg seminar and JSPS seminar series for SciLifeLab
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] ゲノム情報と分子進化学のアプローチを利用して遺伝子レパートリの広がりと進化距離を測る2017

    • Author(s)
      工樂 樹洋
    • Organizer
      第10回Evo-Devo青年の会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] NGSが拓き、分子系統学が照らす「反モデル」生物学への招待2017

    • Author(s)
      工樂 樹洋
    • Organizer
      NGS現場の会、第五回研究会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Remarks] 理化学研究所 生命機能科学研究センター 分子配列比較解析ユニット

    • URL

      http://www.bdr.riken.jp/jp/research/labs/kuraku-s/index.html

    • Related Report
      2017 Research-status Report

URL: 

Published: 2017-04-28   Modified: 2021-02-19  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi