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

Sean P. Gordon, Bruno Contreras-Moreira, Daniel P. Woods, David L. Des Marais, Diane Burgess, Shengqiang Shu, Christoph Stritt, Anne C. Roulin, Wendy Schackwitz, Ludmila Tyler, Joel Martin, Anna Lipzen, Niklas Dochy, Jeremy Phillips, Kerrie Barry, Koen Geuten, Hikmet Budak, Thomas E. Juenger, Richard Amasino, Ana L. Caicedo, David Goodstein, Patrick Davidson, Luis A. J. Mur, Melania Figueroa, Michael Freeling, Pilar Catalan and John P. Vogel ()
Additional contact information
Sean P. Gordon: DOE Joint Genome Institute
Bruno Contreras-Moreira: Estación Experimental de Aula Dei-CSIC
Daniel P. Woods: University of Wisconsin
David L. Des Marais: Harvard University
Diane Burgess: University California, Berkeley
Shengqiang Shu: DOE Joint Genome Institute
Christoph Stritt: University of Zürich
Anne C. Roulin: University of Zürich
Wendy Schackwitz: DOE Joint Genome Institute
Ludmila Tyler: University of Massachusetts Amherst, Institute for Applied Life Sciences
Joel Martin: DOE Joint Genome Institute
Anna Lipzen: DOE Joint Genome Institute
Niklas Dochy: University of Leuven, KU Leuven
Jeremy Phillips: DOE Joint Genome Institute
Kerrie Barry: DOE Joint Genome Institute
Koen Geuten: University of Leuven, KU Leuven
Hikmet Budak: Montana State University
Thomas E. Juenger: University of Texas Austin
Richard Amasino: University of Wisconsin
Ana L. Caicedo: University of Massachusetts Amherst, Institute for Applied Life Sciences
David Goodstein: DOE Joint Genome Institute
Patrick Davidson: DOE Joint Genome Institute
Luis A. J. Mur: Aberystwyth University
Melania Figueroa: University of Minnesota
Michael Freeling: University California, Berkeley
Pilar Catalan: Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC
John P. Vogel: DOE Joint Genome Institute

Nature Communications, 2017, vol. 8, issue 1, 1-13

Abstract: Abstract 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.

Date: 2017
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DOI: 10.1038/s41467-017-02292-8

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