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

Gordon, S.P. ; Contreras-Moreira, B. (Universidad de Zaragoza) ; 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. (Universidad de Zaragoza) ; Vogel, J.P.

Resumen: 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.

Idioma: Inglés

DOI: 10.1038/s41467-020-17302-5

Año: 2020

Publicado en: Nature Communications 11, 1 (2020), 3670 [16 pp]
ISSN: 2041-1723

Factor impacto JCR: 14.919 (2020)

Categ. JCR: MULTIDISCIPLINARY SCIENCES rank: 4 / 73 = 0.055 (2020) - Q1 - T1

Factor impacto SCIMAGO: 5.559 - Biochemistry, Genetics and Molecular Biology (miscellaneous) (Q1) - Physics and Astronomy (miscellaneous) (Q1) - Chemistry (miscellaneous) (Q1)

Financiación: info:eu-repo/grantAgreement/ES/DGA/A01
Financiación: info:eu-repo/grantAgreement/ES/MINECO/CGL2016-79790-P

Tipo y forma: Artículo (Versión definitiva)

Área (Departamento): Área Botánica (Dpto. CC.Agrar.y Medio Natural)