Boulos Chalhoub, Andrew Katz, David Goodstein, Virginia S. Tartaglio, Rubén Sancho, Shengqiang Shu, Vasanth R. Singan, Scott J. Lee, Joel Martin, John H. Doonan, Jerry Jenkins, Sean P. Gordon, Daniel S. Rokhsar, Angelika Czedik-Eysenberg, Luis A. J. Mur, Eugene Goltsman, Kerrie Barry, Samuel P. Hazen, John P. Vogel, Bruno Contreras-Moreira, Antonio Díaz-Pérez, Christopher Plott, Robert Hasterok, Joshua J. Levy, Adam M. Session, Elzbieta Wolny, Jeremy Schmutz, Joanna Lusinska, Armin Djamei, Pilar Catalán, Vinh Ha Dinh-Thi, Candida Nibau, Amy Cartwright, Department of Energy (US), Universidad de Zaragoza, Ministerio de Economía y Competitividad (España), Gobierno de Aragón, National Science Centre (Poland), Leverhulme Trust, European Commission, Austrian Academy of Sciences, Contreras-Moreira, Bruno [0000-0002-5462-907X], Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), United States Department of Energy (DOE)DE-AC02-05CH11231University of Zaragoza FP00006675United States Department of Energy (DOE)FP00006675503504United States Department of Energy (DOE) Spanish Ministry of Economy and Competitiveness CGL2016-79790-PBioflora grant - Spanish Aragon Government A01-17European Social Fund (ESF) National Science Centre, PolandDEC-2012/04/A/NZ3/00572DEC-2014/14/M/NZ2/00519Leverhulme Trust10754European Research Council (ERC)GA335691Austrian Science Fund (FWF)P27429-B22P27818-B22I 3033-B22Austrian Academy of Science (OEAW), and Contreras-Moreira, Bruno
16 Pags.- 8 Figs. This article is licensed under a Creative Commons Attribution 4.0 International License., 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., The work conducted by the US DOE Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract no. DE-AC02-05CH11231 and User Agreement No. FP00006675 between the University of Zaragoza (User) and the DOE (Community Science Program 503504 proposal); S.J. was supported by the DOE Office of Science Graduate Student Research Program; P.C., B.C.-M., A.D.P., and R.S. were supported by a Spanish Ministry of Economy and Competitiveness grant CGL2016-79790-P; P.C., A.D.P., and R.S. were supported by a Bioflora A01-17 grant co-funded by the Spanish Aragon Government and the European Social Fund. R.H., E.W., and J.L. were supported by the National Science Centre Poland (grants DEC-2012/04/A/NZ3/00572 and DEC-2014/14/M/NZ2/00519). J.H.D. and C.N. were supported by Leverhulme Trust (grant no. 10754). A.C.E. and A.D. were supported by the European Research Council under the European Union’s Seventh Framework Program (FP7/2007-2013)/ERC grant agreement no [GA335691 “Effectomics”], the Austrian Science Fund (FWF): [P27429-B22, P27818-B22, I 3033-B22], and the Austrian Academy of Science (OEAW).