doi:10.1038/s41467-020-17302-5engGordon, 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.Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitorsART-2020-119090Our 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.2020http://zaguan.unizar.es/record/9534610.1038/s41467-020-17302-5http://zaguan.unizar.es/record/95346oai:zaguan.unizar.es:95346info:eu-repo/grantAgreement/ES/DGA/A01info:eu-repo/grantAgreement/ES/MINECO/CGL2016-79790-PNature Communications 11, 1 (2020), 3670 [16 pp]byhttp://creativecommons.org/licenses/by/3.0/es/info:eu-repo/semantics/openAccess