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Nat Commun. 2017 Dec 19;8(1):2184. doi: 10.1038/s41467-017-02292-8.

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

Author information

1
DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.
2
Estación Experimental de Aula Dei-CSIC, 50059, Zaragoza, Spain.
3
Fundación ARAID, 50018, Zaragoza, Spain.
4
Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, 500018, Zaragoza, Spain.
5
University of Wisconsin, Madison, WI, 53706, USA.
6
United States Department of Energy Great Lakes Bioenergy Research Center, Madison, WI, 53726, USA.
7
Harvard University, Cambridge, MA, 02138, USA.
8
Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
9
University California, Berkeley, Berkeley, CA, 94720, USA.
10
University of Zürich, Zürich, CH-8006, Switzerland.
11
University of Massachusetts Amherst, Institute for Applied Life Sciences, Amherst, MA, 01003, USA.
12
University of Leuven, KU Leuven, Leuven, 3000, Belgium.
13
Montana State University, Bozeman, MT, 59717, USA.
14
University of Texas Austin, Austin, TX, 78705, USA.
15
Aberystwyth University, Aberystwyth, SY23 3FL, UK.
16
University of Minnesota, St. Paul, MN, 55108, USA.
17
Universidad de Zaragoza-Escuela Politécnica Superior de Huesca, 22071, Huesca, Spain.
18
DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA. jpvogel@lbl.gov.
19
University California, Berkeley, Berkeley, CA, 94720, USA. jpvogel@lbl.gov.

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.

PMID:
29259172
PMCID:
PMC5736591
DOI:
10.1038/s41467-017-02292-8
[Indexed for MEDLINE]
Free PMC Article

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