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

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. Singan, Eugene Goltsman, Kerrie Barry, Vinh Ha Dinh-Thi, Boulos Chalhoub, Antonio Diaz-Perez, Ruben Sancho, Joanna Lusinska, Elzbieta Wolny, Candida Nibau, John H. Doonan, Luis A. J. Mur, Chris Plott, Jerry Jenkins, Samuel P. Hazen, Scott J. Lee, Shengqiang Shu, David Goodstein, Daniel Rokhsar, Jeremy Schmutz, Robert Hasterok, Pilar Catalan () and John P. Vogel ()
Additional contact information
Sean P. Gordon: DOE Joint Genome Institute
Bruno Contreras-Moreira: Estación Experimental de Aula Dei (EEAD-CSIC)
Joshua J. Levy: DOE Joint Genome Institute
Armin Djamei: Gregor Mendel Institute of Molecular Plant Biology GmbH
Angelika Czedik-Eysenberg: Gregor Mendel Institute of Molecular Plant Biology GmbH
Virginia S. Tartaglio: DOE Joint Genome Institute
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)
Antonio Diaz-Perez: Universidad de Zaragoza-Escuela Politécnica Superior de Huesca
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
Jeremy Schmutz: DOE Joint Genome Institute
Robert Hasterok: University of Silesia in Katowice
Pilar Catalan: Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC
John P. Vogel: DOE Joint Genome Institute

Nature Communications, 2020, vol. 11, issue 1, 1-16

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-17302-5

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