Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure
- Gordon, Sean P. [ DOE Joint Genome Institute, Walnut Creek, CA, USA ]
- Contreras-Moreira, Bruno [ Estación Experimental de Aula Dei-CSIC, Zaragoza, Spain; Fundación ARAID, Zaragoza, Spain; Grupo de BioquÃmica, BiofÃsica y BiologÃa Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain ]
- Woods, Daniel P [ University of Wisconsin, Madison, WI, USA; United States Department of Energy Great Lakes Bioenergy Research Center, Madison, WI, USA ]
- Des Marais, David L [ Harvard University, Cambridge, MA, USA; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA ]
- Burgess, Diane [ University California, Berkeley, Berkeley, CA, USA ]
- Shu, Shengqiang [ DOE Joint Genome Institute, Walnut Creek, CA, USA ]
- Stritt, Christoph [ University of Zürich, Zürich, Switzerland ]
- Roulin, Anne C [ University of Zürich, Zürich, Switzerland ]
- Schackwitz, Wendy [ DOE Joint Genome Institute, Walnut Creek, CA, USA ]
- Tyler, Ludmila [ University of Massachusetts Amherst, Institute for Applied Life Sciences, Amherst, MA, USA ]
- Martin, Joel [ DOE Joint Genome Institute, Walnut Creek, CA, USA ]
- Lipzen, Anna [ DOE Joint Genome Institute, Walnut Creek, CA, USA ]
- Dochy, Niklas [ University of Leuven, KU Leuven, Leuven, Belgium ]
- Phillips, Jeremy [ DOE Joint Genome Institute, Walnut Creek, CA, USA ]
- Barry, Kerrie [ DOE Joint Genome Institute, Walnut Creek, CA, USA ]
- Geuten, Koen [ University of Leuven, KU Leuven, Leuven, Belgium ]
- Budak, Hikmet [ Montana State University: Plant Sciences & Plant Pathology ]
- Juenger, Thomas E [ University of Texas Austin, Austin, TX, USA ]
- Goodstein, David [ DOE Joint Genome Institute, Walnut Creek, CA, USA ]
- Davidson, Patrick [ DOE Joint Genome Institute, Walnut Creek, CA, USA ]
- Mur, Luis A J [ Aberystwyth University, Aberystwyth, UK ]
- Figueroa, Melania [ University of Minnesota, St. Paul, MN, USA ]
- Freeling, Michael [ University California, Berkeley, Berkeley, CA, USA ]
- Catalan, Pilar [ Grupo de BioquÃmica, BiofÃsica y BiologÃa Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza, Spain; Universidad de Zaragoza-Escuela Politécnica Superior de Huesca, Huesca, Spain ]
- Vogel, John P [ DOE Joint Genome Institute, Walnut Creek, CA, USA; University California, Berkeley, Berkeley, CA, USA ]
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.