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

Published in:

Nat Commun 11(1) , 3670 (Jul 29 2020)

Author(s):

Gordon, S. P., Contreras-Moreira, B., Levy, J. J., Djamei, A., Czedik-Eysenberg, A., Tartaglio, V. S., Session, A., Martin, J., Cartwright, A., Katz, A., Singan, V. R., Goltsman, E., Barry, K., Dinh-Thi, V. H., Chalhoub, B., Diaz-Perez, A., Sancho, R., Lusinska, J., Wolny, E., Nibau, C., Doonan, J. H., Mur, L. A. J., Plott, C., Jenkins, J., Hazen, S. P., Lee, S. J., Shu, S., Goodstein, D., Rokhsar, D., Schmutz, J., Hasterok, R., Catalan, P., Vogel, J. P.

DOI:

10.1038/s41467-020-17302-5

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.

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