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- Title
Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors.
- Authors
Gordon, 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, Ruben; Lusinska, Joanna; Wolny, Elzbieta; Nibau, Candida
- 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. Existing plant pan-genomic studies usually report considerable intraspecific whole gene presence-absence variation. Here, the authors use pan-genomic approach to reveal gradual polyploid genome evolution by analyzing of Brachypodium hybridum and its diploid progenitors.
- Subjects
POLYPLOIDY; BRACHYPODIUM; GENE expression; RETROTRANSPOSONS
- Publication
Nature Communications, 2020, Vol 11, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-020-17302-5