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Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

Author

Listed:
  • Sean P. Gordon

    (DOE Joint Genome Institute)

  • Bruno Contreras-Moreira

    (Estación Experimental de Aula Dei (EEAD-CSIC)
    Fundación ARAID
    Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC)

  • Joshua J. Levy

    (DOE Joint Genome Institute
    University California, Berkeley)

  • Armin Djamei

    (Gregor Mendel Institute of Molecular Plant Biology GmbH
    Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben. Stadt Seeland)

  • Angelika Czedik-Eysenberg

    (Gregor Mendel Institute of Molecular Plant Biology GmbH)

  • Virginia S. Tartaglio

    (DOE Joint Genome Institute
    University California, Berkeley)

  • Adam Session

    (DOE Joint Genome Institute)

  • Joel Martin

    (DOE Joint Genome Institute)

  • Amy Cartwright

    (DOE Joint Genome Institute)

  • Andrew Katz

    (DOE Joint Genome Institute)

  • Vasanth R. Singan

    (DOE Joint Genome Institute)

  • Eugene Goltsman

    (DOE Joint Genome Institute)

  • Kerrie Barry

    (DOE Joint Genome Institute)

  • Vinh Ha Dinh-Thi

    (Université d’Evry Val d’Essonne (UEVE))

  • Boulos Chalhoub

    (Université d’Evry Val d’Essonne (UEVE)
    Zhejiang University)

  • Antonio Diaz-Perez

    (Universidad de Zaragoza-Escuela Politécnica Superior de Huesca
    Universidad Central de Venezuela)

  • Ruben Sancho

    (Universidad de Zaragoza-Escuela Politécnica Superior de Huesca)

  • Joanna Lusinska

    (University of Silesia in Katowice)

  • Elzbieta Wolny

    (University of Silesia in Katowice)

  • Candida Nibau

    (Aberystwyth University)

  • John H. Doonan

    (Aberystwyth University)

  • Luis A. J. Mur

    (Aberystwyth University)

  • Chris Plott

    (HudsonAlpha Institute for Biotechnology)

  • Jerry Jenkins

    (HudsonAlpha Institute for Biotechnology)

  • Samuel P. Hazen

    (University of Massachusetts Amherst)

  • Scott J. Lee

    (University of Massachusetts Amherst)

  • Shengqiang Shu

    (DOE Joint Genome Institute)

  • David Goodstein

    (DOE Joint Genome Institute)

  • Daniel Rokhsar

    (DOE Joint Genome Institute
    University California, Berkeley)

  • Jeremy Schmutz

    (DOE Joint Genome Institute
    HudsonAlpha Institute for Biotechnology)

  • Robert Hasterok

    (University of Silesia in Katowice)

  • Pilar Catalan

    (Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC
    Universidad de Zaragoza-Escuela Politécnica Superior de Huesca
    Tomsk State University)

  • John P. Vogel

    (DOE Joint Genome Institute
    University California, Berkeley)

Abstract

Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution.

Suggested Citation

  • Sean P. Gordon & Bruno Contreras-Moreira & Joshua J. Levy & Armin Djamei & Angelika Czedik-Eysenberg & Virginia S. Tartaglio & Adam Session & Joel Martin & Amy Cartwright & Andrew Katz & Vasanth R. Si, 2020. "Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-17302-5
    DOI: 10.1038/s41467-020-17302-5
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    Cited by:

    1. Reiko Akiyama & Takao Goto & Toshiaki Tameshige & Jiro Sugisaka & Ken Kuroki & Jianqiang Sun & Junichi Akita & Masaomi Hatakeyama & Hiroshi Kudoh & Tanaka Kenta & Aya Tonouchi & Yuki Shimahara & Jun S, 2023. "Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Chow-Lih Yew & Takashi Tsuchimatsu & Rie Shimizu-Inatsugi & Shinsuke Yasuda & Masaomi Hatakeyama & Hiroyuki Kakui & Takuma Ohta & Keita Suwabe & Masao Watanabe & Seiji Takayama & Kentaro K. Shimizu, 2023. "Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    3. Adam M. Session & Daniel S. Rokhsar, 2023. "Transposon signatures of allopolyploid genome evolution," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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