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

AuthorsGordon, Sean P.; Contreras-Moreira, Bruno ; Levy, Joshua J.; Djamei, Armin; Czedik-Eysenberg, Angelika; Tartaglio, Virginia S.; Session, Adam; Martin, Joel; Cartwright, Amy; Katz, Andrew; Singan, Vasanth R.; Goltsman, Eugene; Barry, Kerrie; Dinh-Thi, Vinh Ha; Chalhoub, Boulos; Diaz-Perez, Antonio; Sancho, Rubén; Lusinka, Joanna; Wolny, Elzbieta; Nibau, Candida; Doonan, John H.; Mur, Luis A. J.; Plott, Chris; Jenkins, Jerry; Hazen, Samuel P.; Lee, Scott J.; Shu, Shengqiang; Goodstein, David; Rokhsar, Daniel; Schmutz, Jeremy; Hasterok, Robert; Catalán, Pilar; Vogel, John P.
Issue DateJul-2020
PublisherNature Publishing Group
CitationGordon SP, Contreras-Moreira B, […] Vogel JP. Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors. Nature Communications 11 (1): 3670 (2020)
AbstractOur 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.
Description16 Pags.- 8 Figs. This article is licensed under a Creative Commons Attribution 4.0 International License.
Publisher version (URL)https://doi.org/10.1038/s41467-020-17302-5
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