TY - JOUR T1 - Extensive gene content variation in theBrachypodium distachyon pan-genome correlateswith population structure JF - Nature Communications Y1 - 2017 A1 - Gordon, Sean P A1 - Contreras-Moreira, Bruno A1 - Woods, Daniel P A1 - Des Marais, David L A1 - Burgess, Diane A1 - Shu, Shengqiang A1 - Stritt, Christopher A1 - Roulin, Anne C A1 - Schackwitz, Wendy A1 - Tyler, Ludmila A1 - Martin, Joel A1 - Lipzen, Anna A1 - Dochy, Niklas A1 - Phillips, Jeremy A1 - Barry, Kerrie A1 - Geuten, Koen A1 - Budak, Hikmet A1 - Juenger, Thomas E A1 - Amasino, Richard A1 - Caicedo, Ana L A1 - Goodstein, David A1 - Davidson, Patrick A1 - Mur, Luis A. J. A1 - Figueroa, Melania A1 - Freeling, Michael A1 - Catalan, Pilar A1 - Vogel, John P AB - While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution. UR - https://www.nature.com/articles/s41467-017-02292-8 IS - 2184 ER -