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Comprehensive analysis of omics adaptability in hybrid species

Planned Research

Project AreaDetermining the principles of the birth of new plant species: molecular elucidation of the lock-and-key systems in sexual reproduction
Project/Area Number 16H06469
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 InstitutionHumanome Lab., Inc. (2020-2021)
National Institute of Advanced Industrial Science and Technology (2016-2019)

Principal Investigator

Sese Jun  株式会社ヒューマノーム研究所, 本社, 代表取締役社長 (40361539)

Co-Investigator(Kenkyū-buntansha) 清水 健太郎  横浜市立大学, 木原生物学研究所, 客員教授 (10742629)
孫 建強  国立研究開発法人農業・食品産業技術総合研究機構, 農業情報研究センター, 主任研究員 (90838624)
Project Period (FY) 2016-06-30 – 2021-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥99,190,000 (Direct Cost: ¥76,300,000、Indirect Cost: ¥22,890,000)
Fiscal Year 2020: ¥18,590,000 (Direct Cost: ¥14,300,000、Indirect Cost: ¥4,290,000)
Fiscal Year 2019: ¥19,110,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥4,410,000)
Fiscal Year 2018: ¥19,110,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥4,410,000)
Fiscal Year 2017: ¥19,500,000 (Direct Cost: ¥15,000,000、Indirect Cost: ¥4,500,000)
Fiscal Year 2016: ¥22,880,000 (Direct Cost: ¥17,600,000、Indirect Cost: ¥5,280,000)
Keywordsハイブリッド / 異質倍数体 / 遺伝子発現 / ゲノム / 機械学習 / 交雑 / 遺伝子発現量 / ハイブリッドゲノム / バイオインフォマティクス / GWAS / 発現解析
Outline of Final Research Achievements

We investigated the molecular basis of the new hybrid ability to adapt to the environment and constructed a method for predicting environmental adaptation. Specifically, (1) Participated in the international consortium of the Wheat 10+ Genome Project and decoded the genome of Norin 61. (2) Constructed a two-step prediction method, which is a machine learning method that predicts phenotypes from the weather. The prediction accuracy was significantly higher than the existing predictions, and it was clarified which meteorological factors affect the phenotype. (3) Conducted a survey on the large-scale genomic change "genome shock" that occurs during hybrids. Within the scope of our study, large-scale genome shock did not occur during hybrids, suggesting that the acquisition of a range of adaptability through gene redundancy is important for the acquisition of environmental adaptability.

Academic Significance and Societal Importance of the Research Achievements

本研究では、ハイブリッド新種の一つとしてコムギをターゲットにした。コムギのゲノム解析を国際コンソーシアムで実施し、世界に先駆けてコムギ全ゲノムを明らかにした。これにより、コムギの育種や気象変動による影響の解析などが進み、気象変動による飢餓の問題などへの対応が進む可能性が高い。一例として、本研究内で人工的な温暖化環境がコムギの成長に与える影響を計測し、さらに機械学習を用いることで、気象変動に対する影響の予測を実施した。

Report

(6 results)
  • 2021 Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (32 results)

All 2021 2019 2018 2017 2016 Other

All Int'l Joint Research (2 results) Journal Article (22 results) (of which Int'l Joint Research: 18 results,  Peer Reviewed: 21 results,  Open Access: 16 results,  Acknowledgement Compliant: 8 results) Presentation (8 results) (of which Int'l Joint Research: 2 results,  Invited: 2 results)

  • [Int'l Joint Research] チューリッヒ大学(スイス)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] University of Agricultural Sciences(インド)

    • Related Report
      2017 Annual Research Report
  • [Journal Article] ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw2021

    • Author(s)
      Milosavljevic Stefan、Kuo Tony、Decarli Samuele、Mohn Lucas、Sese Jun、Shimizu Kentaro K.、Shimizu-Inatsugi Rie、Robinson Mark D.
    • Journal Title

      BMC Genomics

      Volume: 22 Issue: 1 Pages: 547-547

    • DOI

      10.1186/s12864-021-07845-2

    • Related Report
      2020 Annual Research Report
  • [Journal Article] The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests2021

    • Author(s)
      Ng Kevin Siong、Kobayashi MJ.、Fawcett JA.、Hatakeyama M、Paape T、Ng CH、Ang CC、Tnah LH、Lee CT、Nishiyama T、Sese J、O’Brien MJ.、Copetti D、Isa Mohd NM、Ong RC、Putra M、Siregar IZ.、Indrioko S、Kosugi Y、Izuno A、Isagi Y、Lee SL, Shimizu KK.
    • Journal Title

      Communications Biology

      Volume: 4 Issue: 1 Pages: 1166-1166

    • DOI

      10.1038/s42003-021-02682-1

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences.2019

    • Author(s)
      Masashi Tsubaki, Kentaro Tomii, Jun Sese
    • Journal Title

      Bioinformatics

      Volume: 35 Issue: 2 Pages: 309-318

    • DOI

      10.1093/bioinformatics/bty535

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica2018

    • Author(s)
      Paape Timothy、Briskine Roman V.、Halstead-Nussloch Gwyneth、Lischer Heidi E. L.、Shimizu-Inatsugi Rie、Hatakeyama Masaomi、Tanaka Kenta、Nishiyama Tomoaki、Sabirov Renat、Sese Jun、Shimizu Kentaro K.
    • Journal Title

      Nature Communications

      Volume: 9 Issue: 1 Pages: 3909-3909

    • DOI

      10.1038/s41467-018-06108-1

    • NAID

      120007128243

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Molecular basis of flowering under natural long-day conditions in Arabidopsis2018

    • Author(s)
      Young Hun Song, Akane Kubota, Michael S. Kwon, Michael F. Covington, Nayoung Lee, Ella R. Taagen, Dianne Laboy Cintrテウn, Dae Yeon Hwang, Reiko Akiyama, Sarah K. Hodge, He Huang, Nhu H. Nguyen, Dmitri A. Nusinow, Andrew J. Millar, Kentaro K. Shimizu & Takato Imaizumi
    • Journal Title

      Nature Plants

      Volume: 4 Issue: 10 Pages: 824-835

    • DOI

      10.1038/s41477-018-0253-3

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data.2018

    • Author(s)
      Shinya Oki, Tazro Ohta, Go Shioi, Hideki Hatanaka, Osamu Ogasawara, Yoshihiro Okuda, Hideya Kawaji, Ryo Nakaki, Jun Sese, Chikara Meno
    • Journal Title

      EMBO reports

      Volume: 19 Issue: 12

    • DOI

      10.15252/embr.201846255

    • NAID

      120006649027

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Homeolog expression quantification methods for allopolyploids2018

    • Author(s)
      Kuo Tony C Y、Hatakeyama Masaomi、Tameshige Toshiaki、Shimizu Kentaro K、Sese Jun
    • Journal Title

      Briefings in Bioinformatics

      Volume: bby121 Issue: 2 Pages: 395-407

    • DOI

      10.1093/bib/bby121

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] EAGLE: Explicit Alternative Genome Likelihood Evaluator.2017

    • Author(s)
      Tony Kuo, Martin Frith, Jun Sese, Paul Horton
    • Journal Title

      BMC Medical Genomics

      Volume: 11 Issue: Suppl 2 Pages: 28-28

    • DOI

      10.1186/s12920-018-0342-1

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop2017

    • Author(s)
      Hatakeyama M, Aluri S, Balachadran M, Sivarajan S R, Patrignani Andrea、Gr?ter Simon、Poveda Lucy、Shimizu-Inatsugi Rie、Baeten John、Francoijs Kees-Jan、Nataraja Karaba N、Reddy Yellodu AN, Phadnis S, Ravikumar RL, Schlapbach R, Sreeman SM, Shimizu KK
    • Journal Title

      DNA Research

      Volume: 25 Issue: 1 Pages: 39-47

    • DOI

      10.1093/dnares/dsx036

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq.2017

    • Author(s)
      Hirao AS, Onda Y, Shimizu-Inatsugi R, Sese J, Shimizu KK, Kenta T
    • Journal Title

      American Journal of Molecular Biology

      Volume: 7 Pages: 1046-1053

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae).2017

    • Author(s)
      Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh H, Shimizu KK, Isagi Y
    • Journal Title

      Mol Ecol

      Volume: 26 Pages: 1515-1532

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Reference-guided de novo assembly approach improves genome reconstruction for related species2017

    • Author(s)
      Lischer HEL, Shimizu KK
    • Journal Title

      BMC Bioinformatics

      Volume: 18 Pages: 474-474

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Agrobacterium-mediated floral dip transformation of the model polyploid species Arabidopsis kamchatica2017

    • Author(s)
      Yew C-L, Kakui H, Shimizu KK
    • Journal Title

      J Plant Res

      Volume: 9 Pages: 1-10

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Plant adaptive radiation mediated by polyploid plasticity in transcriptomes2017

    • Author(s)
      Shimizu-Inatsugi R, Terada A, Hirose K, Kudos H, Sese J, Shimizu KK
    • Journal Title

      Molecular Ecology

      Volume: 26 Issue: 1 Pages: 193-207

    • DOI

      10.1111/mec.13738

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology2017

    • Author(s)
      Briskine RV, Paape T, Shimizu-Inatsugi R, Nishiyama T, Akama S, Sese J, Shimizu KK
    • Journal Title

      Molecular Ecology Resources

      Volume: 未定 Issue: 5 Pages: 1025-1036

    • DOI

      10.1111/1755-0998.12604

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Genetic diversity of two tropical tree species of the Dipterocarpaceae following logging and restoration in Borneo: high genetic diversity in plots with high species diversity2017

    • Author(s)
      Ang CC, O’brien MJ, Ng KKS, Lee PC, Hector A, Schmid B, Shimizu KK
    • Journal Title

      Plant Ecology & Diversity

      Volume: 9 Issue: 5-6 Pages: 459-469

    • DOI

      10.1080/17550874.2016.1270363

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae)2017

    • Author(s)
      Izuno A,Kitayama K, Onoda Y, Tsuji Y,Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh H, Shimizu KK, Isagi Y
    • Journal Title

      Molecular Ecology

      Volume: 26 Issue: 6 Pages: 1515-1532

    • DOI

      10.1111/mec.14016

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Positional bias in variant calls against draft reference assemblies2017

    • Author(s)
      Briskine RV, Shimizu KK
    • Journal Title

      BMC Genomics

      Volume: 18 Issue: 1 Pages: 263-263

    • DOI

      10.1186/s12864-017-3637-2

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] LAMPLINK: detection of statistically significant SNP combinations from GWAS data2016

    • Author(s)
      Aika Terada, Ryo Yamada, Koji Tsuda, Jun Sese
    • Journal Title

      Bioinformatics

      Volume: 32 Issue: 22 Pages: 3513-3515

    • DOI

      10.1093/bioinformatics/btw418

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism2016

    • Author(s)
      Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, Guggisberg A, Paape T, Schmid K, Fedorenko OM, Holm S, Sll T, Schltterer C, Marhold K, Widmer A, Sese J, Shimizu KK, Weigel D, Krmer U, Koch MA, Nordborg M
    • Journal Title

      Nature Genetics

      Volume: 48 Issue: 9 Pages: 1077-1082

    • DOI

      10.1038/ng.3617

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica2016

    • Author(s)
      Paape T, Hatakeyama M, Shimizu-Inatsugi R, Cereghetti T, Onda Y, Kenta T, Sees J, Shimizu KK
    • Journal Title

      Molecular biology and evolution

      Volume: 33 Issue: 11 Pages: 2781-2800

    • DOI

      10.1093/molbev/msw141

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] The Cardamine hirsuta genome offers insight into the evolution of morphological diversity2016

    • Author(s)
      Gan X, Hay A, Kwantes M, Haberer G (31人中21番目)
    • Journal Title

      Nature Plants

      Volume: 2 Issue: 11 Pages: 16167-16167

    • DOI

      10.1038/nplants.2016.167

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] Time-course image analysis of Arabidopsis thaliana and its wild relatives in fluctuating field conditions using machine learning2021

    • Author(s)
      Reiko Akiyama, Takao Goto, Toshiaki Tameshige, Jiro Sugisaka, Rie Shimizu-Inatsugi, Jianqiang Sun, Junichi Akita, Natsumaro Kutsuna, Jun Sese, Kentaro K. Shimizu
    • Organizer
      Patterns in Nature and Plant Sciences; PSC SYMPOSIUM 2021
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 異質倍数体の育種に向けたマルチオミクス解析2019

    • Author(s)
      瀬々 潤
    • Organizer
      植物細胞分子生物学会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Decoding cellular functions by AI with large-scale collection of genetic information2019

    • Author(s)
      Jun Sese
    • Organizer
      Molecular Biology Society Japan
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A dominant mutation conferred self-compatibility in allotetraploid A.kamuchatica2017

    • Author(s)
      Yew C.L., Tsuchimatsu T., Shimizu-Inatsugi R., Shimizu K.K.
    • Organizer
      Symposium on “Detecting the Genomic Signal of Polygenic Adaptation and the Role of Epistasis in Evolution”
    • Related Report
      2017 Annual Research Report
  • [Presentation] Identification of a gene controlling pollen number by a GWAS and CRISPR mutants2017

    • Author(s)
      Kakui H., Tsuchimatsu T., Yamazaki M., Marona C., Tsutsui H., Hedhly A., Meng D., Sato Y., Stadler T., Grossniklaus U., Kanaoka M., Lenhard M., Nordborg M., Shimizu K
    • Organizer
      Symposium on “Detecting the Genomic Signal of Polygenic Adaptation and the Role of Epistasis in Evolution”
    • Related Report
      2017 Annual Research Report
  • [Presentation] Multiple hybrid de novo genome assembly of finger millet2017

    • Author(s)
      Hatakeyama M., Aluri S., Patrignani A., Grter S., Poveda L., Schlapbach R., Shimizu-Inatsugi R., Shimizu K.K., Baeten J.B., Francoijs K.-J., Balachadran M.T., Sivarajan SR, Nataraja K.N., Ravikumar R.L., Reddy Y.A.N., Sreeman SM
    • Organizer
      Zurich-Basel Plant Science Center PSC symposium
    • Related Report
      2017 Annual Research Report
  • [Presentation] A single dominant mutateon conferred self-compatibility in allotetraploid Arabidopsis kamchatica2017

    • Author(s)
      Yew C.L., Tsuchimatsu T., Shimizu-Inatsugi R., Shimizu K.K.
    • Organizer
      Zurich-Basel Plant Science Center PSC symposium,
    • Related Report
      2017 Annual Research Report
  • [Presentation] Identification and transcriptome analysis of pollen number controlling gene, RDP12017

    • Author(s)
      Kakui H.
    • Organizer
      Zurich-Basel Plant Science Center PSC symposium
    • Related Report
      2017 Annual Research Report

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Published: 2016-07-04   Modified: 2023-01-30  

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