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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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
Issue number1
Publication statusPublished - 29 Jul 2020


  • 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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