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Measuring molecular fluctuation of chordate developmental system and its contribution toward evolutionary conservation

Planned Research

Project AreaEvolutionary theory for constrained and directional diversities
Project/Area Number 17H06387
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 University of Tokyo

Principal Investigator

Irie Naoki  東京大学, 大学院理学系研究科(理学部), 准教授 (10536121)

Co-Investigator(Kenkyū-buntansha) 上坂 将弘  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, 研究員 (20756499)
Project Period (FY) 2017-06-30 – 2022-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥145,340,000 (Direct Cost: ¥111,800,000、Indirect Cost: ¥33,540,000)
Fiscal Year 2021: ¥22,880,000 (Direct Cost: ¥17,600,000、Indirect Cost: ¥5,280,000)
Fiscal Year 2020: ¥24,830,000 (Direct Cost: ¥19,100,000、Indirect Cost: ¥5,730,000)
Fiscal Year 2019: ¥26,520,000 (Direct Cost: ¥20,400,000、Indirect Cost: ¥6,120,000)
Fiscal Year 2018: ¥29,380,000 (Direct Cost: ¥22,600,000、Indirect Cost: ¥6,780,000)
Fiscal Year 2017: ¥41,730,000 (Direct Cost: ¥32,100,000、Indirect Cost: ¥9,630,000)
Keywords進化 / 進化発生生物学 / 発生拘束 / ゆらぎ / 発生安定性 / 頑健性 / 進化生物学 / 発生生物学 / 安定性 / 発生 / バイオインフォマティクス / EvoDevo / 反復説 / 砂時計モデル / 比較発生 / ゲノム / エピジェネティクス / 進化可能性 / 進化発生学
Outline of Final Research Achievements

This project examined whether fluctuations in the developmental process of chordates contribute to evolutionary conservation (constraints and directions). The results of the study suggested that the developmental stage in which the basic structure of vertebrates is constructed is developmentally stable, showing small fluctuations in gene expression profiles. In addition, we found that this may be one of the contributing factors to the evolutionary conservation of this developmental phase. The experimental data also showed that body plan developing stage is enriched with repeatedly used genes, and this could have contributed to the evolutionary conservation of the body plan developing phase. This also suggests that while gene co-option frequently took place to facilitate the acquisition of new traits, it may also work as a factor that limits phenotypic diversification.

Academic Significance and Societal Importance of the Research Achievements

これまでの進化生物学は、遺伝的変異や環境の影響で出現した多用な特徴(表現型)が選択されたり、偶発的に集団内にひろがることで起こると説明されてきた。一方で、今回の一連の研究は、生物そのものにどの程度特徴を変えられるかという多様化のポテンシャルが備わっていることを示すものであり、その具体的実態(揺らぎ、遺伝子の使いまわしなど)を解明した研究である。様々な表現型のバリエーションを生み出すポテンシャルが低いと結果的に多様化する機会が減るというのは自然な考えであるものの、具体的にこうしたメカニズムまで明らかとなったのは大きな成果だと考えている。

Report

(6 results)
  • 2022 Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (53 results)

All 2023 2022 2021 2020 2019 2018 2017 Other

All Int'l Joint Research (6 results) Journal Article (17 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 17 results,  Open Access: 15 results) Presentation (26 results) (of which Int'l Joint Research: 12 results,  Invited: 21 results) Remarks (3 results) Funded Workshop (1 results)

  • [Int'l Joint Research] Boston University/California Institute of Technology/Brown University(米国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] Kunming Institute of Zoology/Yunnan Agricultural University/Chinese Academy of Sciences(中国)

    • Related Report
      2020 Annual Research Report
  • [Int'l Joint Research] BGI/PICB(中国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Boston University(米国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] 昆明動物学研究所(中国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] ボストン大学/ブラウン大学(米国)

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Stability in gene expression and body-plan development leads to evolutionary conservation.2023

    • Author(s)
      Yui Uchida*, Hiroyuki Takeda, Chikara Furusawa & Naoki Irie*
    • Journal Title

      EvoDevo

      Volume: vol. 14, no.4 Issue: 1

    • DOI

      10.1186/s13227-023-00208-w

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The pentameric hydrocoel lobes organize adult pentameral structures in a sea cucumber, Apostichopus japonicus2022

    • Author(s)
      Udagawa Sumio、Nagai Akiko、Kikuchi Mani、Omori Akihito、Tajika Atsushi、Saito Mieko、Miura Toru、Irie Naoki、Kamei Yasuhiro、Kondo Mariko
    • Journal Title

      Developmental Biology

      Volume: 492 Pages: 71-78

    • DOI

      10.1016/j.ydbio.2022.09.002

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Potential contribution of intrinsic developmental stability toward body plan conservation2022

    • Author(s)
      Uchida Yui、Shigenobu Shuji、Takeda Hiroyuki、Furusawa Chikara、Irie Naoki
    • Journal Title

      BMC Biology

      Volume: 20 Issue: 1 Pages: 82-82

    • DOI

      10.1186/s12915-022-01276-5

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Distinguishing Evolutionary Conservation from Derivedness.2022

    • Author(s)
      Jason Cheok Kuan Leong*, Masahiro Uesaka, Naoki Irie*
    • Journal Title

      Life

      Volume: 12(3), 440 Issue: 3 Pages: 440-440

    • DOI

      10.3390/life12030440

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Measuring potential effects of the developmental burden associated with the vertebrate notochord.2022

    • Author(s)
      Fujimoto S, Yamanaka K, Tanegashima C, Nishimura O, Kuraku S, Kuratani S, and Irie N.
    • Journal Title

      J Exp Zool B Mol Dev Evol.

      Volume: 338 Issue: 1-2 Pages: 129-136

    • DOI

      10.1002/jez.b.23032

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms2021

    • Author(s)
      Jason Cheok Kuan Leong*, Yongxin Li, Masahiro Uesaka, Yui Uchida, Akihito Omori, Meng Hao, Wenting Wan, Yang Dong, Yandong RenSi Zhang, Tao Zeng, Fayou Wang, Luonan Chen, Gary Wessel, Brian T. Livingston, Cynthia Bradham, Wen Wang, Naoki Irie*
    • Journal Title

      Front. Cell Dev. Biol.

      Volume: 26

    • DOI

      10.3389/fcell.2021.749963

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The developmental hourglass model and recapitulation: An attempt to integrate the two models.2021

    • Author(s)
      Uesaka, M., Kuratani, S., and Irie, N.
    • Journal Title

      J Exp Zool B Mol Dev Evol.

      Volume: in press Issue: 1-2 Pages: 1-11

    • DOI

      10.1002/jez.b.23027

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] How can recapitulation be reconciled with modern concepts of evolution?2021

    • Author(s)
      Kuratani S, Uesaka M, Irie N.
    • Journal Title

      J Exp Zool B Mol Dev Evol.

      Volume: in press Issue: 1-2 Pages: 1-8

    • DOI

      10.1002/jez.b.23020

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genomic insights of body plan transitions from bilateral to pentameric symmetry in Echinoderms2020

    • Author(s)
      Yongxin Li, et al. (35名中 35番目 Naoki Irie*)
    • Journal Title

      Communications Biology

      Volume: 3:371 Issue: 1 Pages: 371-371

    • DOI

      10.1038/s42003-020-1091-1

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Toward understanding of evolutionary constraints: experimental and theoretical approaches2020

    • Author(s)
      Chikara Furusawa*, Naoki Irie*
    • Journal Title

      Biophysical Reviews

      Volume: 12 Issue: 5 Pages: 1155-1161

    • DOI

      10.1007/s12551-020-00708-2

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes2020

    • Author(s)
      John D. Hogan, et al. (Naoki Irie 19名中16番目)
    • Journal Title

      Developmental Biology

      Volume: 460:2 Issue: 2 Pages: 139-154

    • DOI

      10.1016/j.ydbio.2019.12.002

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Recapitulation-like developmental transitions of chromatin accessibility in vertebrates2019

    • Author(s)
      Uesaka Masahiro、Kuratani Shigeru、Takeda Hiroyuki、Irie Naoki
    • Journal Title

      Zoological Letters

      Volume: 5 Issue: 1 Pages: 33-33

    • DOI

      10.1186/s40851-019-0148-9

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The phylum Vertebrata: a case for zoological recognition.2018

    • Author(s)
      Irie, N., Kuratani, S., and Satoh, N.
    • Journal Title

      Zoological Lett

      Volume: 4 Issue: 1 Pages: 32-32

    • DOI

      10.1186/s40851-018-0114-y

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Embryonic lethality is not sufficient to explain hourglass-like conservation of vertebrate embryos2018

    • Author(s)
      Yui Uchida, Masahiro Uesaka, Takayoshi Yamamoto, Hiroyuki Takeda and Naoki Irie
    • Journal Title

      EvoDevo

      Volume: 9:7 Issue: 1 Pages: 1-11

    • DOI

      10.1186/s13227-018-0095-0

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Centromere evolution and CpG methylation during vertebrate speciation2017

    • Author(s)
      Kazuki Ichikawa, Shingo Tomioka, Yuta Suzuki, Ryohei Nakamura, Koichiro Doi, Jun Yoshimura, Masahiko Kumagai, Yusuke Inoue, Yui Uchida, Naoki Irie, Hiroyuki Takeda* & Shinich Morishita*
    • Journal Title

      Nature Communications

      Volume: 1833 Issue: 1 Pages: 1722-1730

    • DOI

      10.1038/s41467-017-01982-7

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Weighted gene co-expression network analysis reveals potential genes involved in early metamorphosis process in sea cucumber Apostichopus japonicus2017

    • Author(s)
      Yongxin Li, Mani Kikuchi, Xueyan Li, Qionghua Gao, Zijun Xiong, Yandong Ren, Ruoping Zhao, Bingyu Mao, Mariko Kondo, Naoki Irie, Wen Wang*
    • Journal Title

      BBRC

      Volume: 495:1 Issue: 1 Pages: 1395-1402

    • DOI

      10.1016/j.bbrc.2017.11.154

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Constrained vertebrate evolution by pleiotropic genes.2017

    • Author(s)
      Hu H, Uesaka M, Guo S, Shimai K, Lu TM, Li F, Fujimoto S, Ishikawa M, Liu S, Sasagawa Y, Zhang G, Kuratani S, Yu JK, Kusakabe TG, Khaitovich P, Irie N; EXPANDE Consortium.
    • Journal Title

      Nat Ecol Evol

      Volume: 1 Issue: 11 Pages: 1722-1730

    • DOI

      10.1038/s41559-017-0318-0

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] 動物の解剖学的基本パターンはなぜ進化的に保守的なのか2022

    • Author(s)
      入江直樹
    • Organizer
      第127 回日本解剖学会総会・全国学術集会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Can we predict evolutionary outcome of animal body plan?2021

    • Author(s)
      Naoki Irie
    • Organizer
      International Congress of Zoology Cape Town
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Internal factors of biological system that biases evolutionary outcome2021

    • Author(s)
      Naoki Irie
    • Organizer
      ICG-16, Qindao
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Possible constraints by developmental robustness2021

    • Author(s)
      Naoki Irie
    • Organizer
      2nd AsiaEvo
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 発生頑健性による進化の慣性力2021

    • Author(s)
      入江直樹
    • Organizer
      日本分子生物学会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Developmental robustness may bias macroevolutionary outcome2020

    • Author(s)
      Naoki Irie
    • Organizer
      17th Spanish Society for Developmental Biology Meeting (Spain, online)
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 動物表現型進化の予測にむけて2020

    • Author(s)
      入江直樹
    • Organizer
      ExCELLS シンポジウム
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] 動物ボディプランにみられる進化的慣性力の仕組みは?2020

    • Author(s)
      入江直樹
    • Organizer
      日本進化学会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] 遺伝子の使い回しは多様化にとって諸刃の剣か2020

    • Author(s)
      入江直樹
    • Organizer
      日本分子生物学会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Potential double-edged sword effect of gene re-usage toward evolutionary diversification2019

    • Author(s)
      Naoki Irie
    • Organizer
      Molecular Biology Society of Japan
    • Related Report
      2019 Annual Research Report
  • [Presentation] Possible bias toward micro- and macro-evolutionary conservation by developmental systems2019

    • Author(s)
      Naoki Irie
    • Organizer
      Workshoo reconciling micro-macro evolution (Oslo)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Do echinoderm embryos follow hourglass-like divergence?2019

    • Author(s)
      Naoki Irie
    • Organizer
      ICG-Ocean 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] What makes animal embryos to follow the hourglass model?2019

    • Author(s)
      Naoki Irie
    • Organizer
      日本生物物理学会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Could have “small phenotypic fluctuation” contributed to the evolutionary conservation in vertebrate embryogenesis?2019

    • Author(s)
      Yui Uchida, Naoki Irie
    • Organizer
      21st Annual Meeting of the Society of Evolutionary Studies, Japan
    • Related Report
      2019 Annual Research Report
  • [Presentation] Development and Evolution2019

    • Author(s)
      Naoki Irie
    • Organizer
      SERB School in Evolutionary Biology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The developmental hourglass model in animal embryogenesis2018

    • Author(s)
      Naoki Irie
    • Organizer
      Developmental Biology of Sea Urchin and other Marine Invertebrates
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Cost of complexity” contributed to the vertebrate bodyplan conservation?2018

    • Author(s)
      Naoki Irie
    • Organizer
      Euro EvoDevo
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Gene re-usages constrained the evolvability of animal bodyplan?2018

    • Author(s)
      Naoki Irie
    • Organizer
      EvoDevo Seminar series, Cambridge University
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] “Cost of complexity” hypothesis supported in animal embryonic evolution?2018

    • Author(s)
      Naoki Irie
    • Organizer
      The 1st AsiaEvo conference
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 遺伝子の使い回しは進化にとって諸刃の剣か?2018

    • Author(s)
      入江直樹
    • Organizer
      再生学異分野融合研究会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 表現型揺らぎから探る進化の方向性と拘2018

    • Author(s)
      入江直樹
    • Organizer
      日本進化学会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 複雑な遺伝子制御を持つ動物ほど進化可能性が低いかもしれない2018

    • Author(s)
      入江直樹
    • Organizer
      生命の起源および進化学会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] In search for a general law of animal embryonic evolution?2017

    • Author(s)
      Naoki Irie
    • Organizer
      he 12th International Workshop on Advanced Genomics [12AGW]
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] What are the potential mechanisms that made vertebrates’ bodyplan conserved?2017

    • Author(s)
      Naoki Irie
    • Organizer
      50th Anniversary Meeting of Japanese Society of Developmental Biologists
    • Related Report
      2017 Annual Research Report
  • [Presentation] The developmental hourglass model: the law of embryonic evolution?2017

    • Author(s)
      Naoki Irie
    • Organizer
      From Genetic Networks to a Cellular Wiring Diagram
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 複雑な遺伝子制御を持つ動物ほど進化可能性が低いかもしれない2017

    • Author(s)
      Naoki Irie
    • Organizer
      生命の起源および進化学会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Remarks] 入江直樹研究室

    • URL

      http://www.bs.s.u-tokyo.ac.jp/~hassei/irie/index.html#home

    • Related Report
      2018 Annual Research Report
  • [Remarks] 新学術領域 進化制約方向性

    • URL

      http://constrained-evo.org/

    • Related Report
      2017 Annual Research Report
  • [Remarks] 研究室ウェブサイト

    • URL

      http://www.bs.s.u-tokyo.ac.jp/~hassei/irie/index.html#home

    • Related Report
      2017 Annual Research Report
  • [Funded Workshop] CDE Open Online Seminar series(1 ~ 3回)2020

    • Related Report
      2020 Annual Research Report

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Published: 2017-07-04   Modified: 2024-01-30  

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