TY - JOUR
T1 - Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure
AU - Gordon, Sean P.
AU - Contreras-Moreira, Bruno
AU - Woods, Daniel P.
AU - Des Marais, David L.
AU - Burges, Diane
AU - Shu, Shengqiang
AU - Stritt, Christoph
AU - Roulin, Anne C.
AU - Schackwitz, Wendy
AU - Tyler, Ludmila
AU - Martin, Joel
AU - Lipzen, Anna
AU - Dochy, Niklas
AU - Phillips, Jeremy
AU - Barry, Kerrie
AU - Geuten, Koen
AU - Budak, Hikmet
AU - Jeunger, Thomas E.
AU - Amasino, Richard
AU - Caicedo, Ana L.
AU - Goodstein, David
AU - Davidson, Patrick
AU - Mur, Luis
AU - Figueroa, Melania
AU - Freeling, Michael
AU - Catalán, Pilar
AU - Vogel, John P.
PY - 2017/12/19
Y1 - 2017/12/19
N2 - 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.
AB - 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.
KW - comparative genomics
KW - plant genetics
KW - structural variation
UR - https://www.nature.com/articles/s41467-017-02292-8#Sec20
U2 - 10.1038/s41467-017-02292-8
DO - 10.1038/s41467-017-02292-8
M3 - Article
SN - 2041-1723
VL - 8
JO - Nature Communications
JF - Nature Communications
IS - N/A
M1 - 2184
ER -
