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 NibauJohn 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, John P Vogel

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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.

Original languageEnglish
Article number3670
Number of pages16
JournalNature Communications
Volume11
Issue number1
DOIs
Publication statusPublished - 29 Jul 2020

Keywords

  • Brachypodium/genetics
  • Chromosomes, Plant/genetics
  • Diploidy
  • Evolution, Molecular
  • Genome, Chloroplast
  • Genome, Plant
  • Genomics
  • Hybridization, Genetic
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • Polyploidy
  • Retroelements/genetics
  • Species Specificity

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