Adaptation of S. cerevisiae to fermented food environments reveals remarkable genome plasticity and the footprints of domestication

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• dc.contributor.author Legras, Jean-Luc
• dc.contributor.author Galeote, Virginie
• dc.contributor.author Bigey, Frédéric
• dc.contributor.author Camarasa, Carole
• dc.contributor.author Marsit, Souhir
• dc.contributor.author Nidelet, Thibault
• dc.contributor.author Sanchez, Isabelle
• dc.contributor.author Couloux, Arnaud
• dc.contributor.author Guy, Julie
• dc.contributor.author Franco-Duarte, Ricardo
• dc.contributor.author Marcet Houben, Marina
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
• dc.contributor.author Schuller, Dorit
• dc.contributor.author Sampaio, José Paulo
• dc.contributor.author Dequin, Sylvie
• dc.date.accessioned 2019-11-22T08:54:17Z
• dc.date.available 2019-11-22T08:54:17Z
• dc.date.issued 2018
• dc.description.abstract The budding yeast Saccharomyces cerevisiae can be found in the wild and is also frequently associated with human activities. Despite recent insights into the phylogeny of this species, much is still unknown about how evolutionary processes related to anthropogenic niches have shaped the genomes and phenotypes of S. cerevisiae. To address this question, we performed population-level sequencing of 82 S. cerevisiae strains from wine, flor, rum, dairy products, bakeries, and the natural environment (oak trees). These genomic data enabled us to delineate specific genetic groups corresponding to the different ecological niches and revealed high genome content variation across the groups. Most of these strains, compared with the reference genome, possessed additional genetic elements acquired by introgression or horizontal transfer, several of which were population-specific. In addition, several genomic regions in each population showed evidence of nonneutral evolution, as shown by high differentiation, or of selective sweeps including genes with key functions in these environments (e.g., amino acid transport for wine yeast). Linking genetics to lifestyle differences and metabolite traits has enabled us to elucidate the genetic basis of several niche-specific population traits, such as growth on galactose for cheese strains. These data indicate that yeast has been subjected to various divergent selective pressures depending on its niche, requiring the development of customized genomes for better survival in these environments. These striking genome dynamics associated with local adaptation and domestication reveal the remarkable plasticity of the S. cerevisiae genome, revealing this species to be an amazing complex of specialized populations.
• dc.format.mimetype application/pdf
• dc.identifier.citation Legras JL, Galeote V, Bigey F, Camarasa C, Marsit S, Nidelet T et al. cerevisiae to fermented food environments reveals remarkable genome plasticity and the footprints of domestication. Mol Biol Evol. 2018;35(7):1712-27. DOI: 10.1093/molbev/msy066
• dc.identifier.doi http://dx.doi.org/10.1093/molbev/msy066
• dc.identifier.issn 0737-4038
• dc.identifier.uri http://hdl.handle.net/10230/42933
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Molecular Biology and Evolution. 2018;35(7):1712-27
• dc.rights © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
• dc.subject.keyword Saccharomyces cerevisiae
• dc.subject.keyword Adaptation
• dc.subject.keyword Domestication
• dc.subject.keyword Sweep
• dc.subject.keyword Horizontal gene transfer
• dc.title Adaptation of S. cerevisiae to fermented food environments reveals remarkable genome plasticity and the footprints of domestication
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion