Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

• Published in: Nature communications Vol. 8; no. 1; pp. 2184 - 13
• Main Authors: Gordon, Sean P., Contreras-Moreira, Bruno, Woods, Daniel P., Des Marais, David L., Burgess, Diane, Shu, Shengqiang, Stritt, Christoph, Roulin, Anne C., Schackwitz, Wendy, Tyler, Ludmila, Martin, Joel, Lipzen, Anna, Dochy, Niklas, Phillips, Jeremy, Barry, Kerrie, Geuten, Koen, Budak, Hikmet, Juenger, Thomas E., Amasino, Richard, Caicedo, Ana L., Goodstein, David, Davidson, Patrick, Mur, Luis A. J., Figueroa, Melania, Freeling, Michael, Catalan, Pilar, Vogel, John P.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19.12.2017; Nature Publishing Group; Nature Portfolio
• Subjects: 631/208/212/748; 631/208/726/649/2157; 631/449/2491; Annotations; BASIC BIOLOGICAL SCIENCES; Biological evolution; Biological Variation, Population - genetics; Brachypodium - genetics; Brachypodium distachyon; Chromosomes, Plant - genetics; Comparative genomics; DNA Transposable Elements - genetics; Eukaryotes; Evolution, Molecular; Genes; Genetic Variation - genetics; Genetics; Genome, Plant - genetics; Genomes; Grasses; Humanities and Social Sciences; multidisciplinary; Phenotypic variations; Phylogeny; Plant genetics; Population genetics; Population structure; Science; Science (multidisciplinary); Structural variation; Synteny; Synteny - genetics
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-017-02292-8

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. The role of differential gene content in the evolution and function of eukaryotic genomes remains poorly explored. Here the authors assemble and annotate the Brachypodium distachyon pan-genome consisting of 54 diverse lines and reveal the differential present genes as a major driver of phenotypic variation.