Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure
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.
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- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Estacion Experimental de Aula Dei-CSIC, Zaragoza (Spain); Fundacion ARAID, Zaragoza (Spain); Unidad Asociada al CSIC, Zaragoza (Spain)
- Univ. of Wisconsin, Madison, WI (United States); United States Dept. of Energy Great Lakes Bioenergy Research Center, Madison, WI (United States)
- Harvard Univ., Cambridge, MA (United States); Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
- Univ. of California, Berkeley, CA (United States)
- Univ. of Zurich, Zurich (Switzerland)
- Univ. of Massachusetts, Amherst, MA (United States)
- Univ. of Leuven, Leuven (Belgium)
- Montana State Univ., Bozeman, MT (United States)
- Univ. of Texas Austin, Austin, TX (United States)
- Aberystwyth Univ., Aberystwyth (United Kingdom)
- Univ. of Minnesota, St. Paul, MN (United States)
- Unidad Asociada al CSIC, Zaragoza (Spain); Univ. de Zaragoza-Escuela Politecnica Superior de Huesca, Huesca (Spain)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1436654
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Comparative genomics; Plant genetics; Structural variation
Citation Formats
Gordon, Sean P., Contreras-Moreira, Bruno, Woods, Daniel P., Des Marais, David L., Burgess, Diane, Shu, Shengqiang, Stritt, Christoph, Roulin, Anne C., Schackwitz, Wendy, Tyler, Ludmila, Martin, Joel, Lipzen, Anna, Dochy, Niklas, Phillips, Jeremy, Barry, Kerrie, Geuten, Koen, Budak, Hikmet, Juenger, Thomas E., Amasino, Richard, Caicedo, Ana L., Goodstein, David, Davidson, Patrick, Mur, Luis A. J., Figueroa, Melania, Freeling, Michael, Catalan, Pilar, and Vogel, John P. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. United States: N. p., 2017.
Web. doi:10.1038/s41467-017-02292-8.
Gordon, Sean P., Contreras-Moreira, Bruno, Woods, Daniel P., Des Marais, David L., Burgess, Diane, Shu, Shengqiang, Stritt, Christoph, Roulin, Anne C., Schackwitz, Wendy, Tyler, Ludmila, Martin, Joel, Lipzen, Anna, Dochy, Niklas, Phillips, Jeremy, Barry, Kerrie, Geuten, Koen, Budak, Hikmet, Juenger, Thomas E., Amasino, Richard, Caicedo, Ana L., Goodstein, David, Davidson, Patrick, Mur, Luis A. J., Figueroa, Melania, Freeling, Michael, Catalan, Pilar, & Vogel, John P. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. United States. https://doi.org/10.1038/s41467-017-02292-8
Gordon, Sean P., Contreras-Moreira, Bruno, Woods, Daniel P., Des Marais, David L., Burgess, Diane, Shu, Shengqiang, Stritt, Christoph, Roulin, Anne C., Schackwitz, Wendy, Tyler, Ludmila, Martin, Joel, Lipzen, Anna, Dochy, Niklas, Phillips, Jeremy, Barry, Kerrie, Geuten, Koen, Budak, Hikmet, Juenger, Thomas E., Amasino, Richard, Caicedo, Ana L., Goodstein, David, Davidson, Patrick, Mur, Luis A. J., Figueroa, Melania, Freeling, Michael, Catalan, Pilar, and Vogel, John P. Tue .
"Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure". United States. https://doi.org/10.1038/s41467-017-02292-8. https://www.osti.gov/servlets/purl/1436654.
@article{osti_1436654,
title = {Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure},
author = {Gordon, Sean P. and Contreras-Moreira, Bruno and Woods, Daniel P. and Des Marais, David L. and Burgess, Diane and Shu, Shengqiang and Stritt, Christoph and Roulin, Anne C. and Schackwitz, Wendy and Tyler, Ludmila and Martin, Joel and Lipzen, Anna and Dochy, Niklas and Phillips, Jeremy and Barry, Kerrie and Geuten, Koen and Budak, Hikmet and Juenger, Thomas E. and Amasino, Richard and Caicedo, Ana L. and Goodstein, David and Davidson, Patrick and Mur, Luis A. J. and Figueroa, Melania and Freeling, Michael and Catalan, Pilar and Vogel, John P.},
abstractNote = {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.},
doi = {10.1038/s41467-017-02292-8},
journal = {Nature Communications},
number = 1,
volume = 8,
place = {United States},
year = {2017},
month = {12}
}
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- Woods, Daniel; Dong, Yinxin; Bouche, Frederic
- eLife, Vol. 8
Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants
journal, May 2020
- Christian, Ryan W.; Hewitt, Seanna L.; Roalson, Eric H.
- Scientific Reports, Vol. 10, Issue 1
Computational aspects underlying genome to phenome analysis in plants
text, January 2019
- Bolger, Anthony M.; Poorter, Hendrik; Dumschott, Kathryn
- RWTH Aachen University
DNA-Based Assessment of Genetic Diversity in Grassland Plant Species: Challenges, Approaches, and Applications
text, January 2019
- Loera-Sánchez, Miguel; Studer, Bruno; Kölliker, Roland
- ETH Zurich
Evolution of Conserved Noncoding Sequences in Arabidopsis thaliana
journal, February 2021
- Yocca, Alan E.; Lu, Zefu; Schmitz, Robert J.
- Molecular Biology and Evolution, Vol. 38, Issue 7