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

Authors Organisations
  • Sean P. Gordon(Author)
    Joint Genome Institute
  • Bruno Contreras-Moreira(Author)
    Estación Experimental de Aula Dei-CSIC
    Fundación ARAID
  • Daniel P. Woods(Author)
    University of Wisconsin-Madison
  • David L. Des Marais(Author)
    Harvard University
    MIT - Massachusetts Institute of Technology
  • Diane Burges(Author)
    University of California, Berkeley
  • Shengqiang Shu(Author)
    Joint Genome Institute
  • Christoph Stritt(Author)
    University of Zurich
  • Anne C. Roulin(Author)
    University of Zurich
  • Wendy Schackwitz(Author)
    Joint Genome Institute
  • Ludmila Tyler(Author)
    University of Massachusetts Amherst
  • Joel Martin(Author)
    Joint Genome Institute
  • Anna Lipzen(Author)
    Joint Genome Institute
  • Niklas Dochy(Author)
    KU Leuven
  • Jeremy Phillips(Author)
    Joint Genome Institute
  • Kerrie Barry(Author)
    Joint Genome Institute
  • Koen Geuten(Author)
    KU Leuven
  • Hikmet Budak(Author)
    Montana State University
  • Thomas E. Jeunger(Author)
    University of Texas
  • Richard Amasino(Author)
    University of Wisconsin-Madison
  • Ana L. Caicedo(Author)
    University of Massachusetts Amherst
  • David Goodstein(Author)
    Joint Genome Institute
  • Patrick Davidson(Author)
    Joint Genome Institute
  • Luis Mur(Author)
  • Melania Figueroa(Author)
    University of Minnesota
  • Michael Freeling(Author)
    University of California, Berkeley
  • Pilar Catalán(Author)
    University of Zaragoza
  • John P. Vogel(Author)
    Joint Genome Institute
    University of California, Berkeley
Type Article
Original languageEnglish
Article number2184
JournalNature Communications
Early online date19 Dec 2017
Publication statusE-pub ahead of print - 19 Dec 2017
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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


  • comparative genomics, plant genetics, structural variation