Genome evolution across 1,011 Saccharomyces cerevisiae isolates

Jackson Peter, Matteo De Chiara, Anne Friedrich, Jia-Xing Yue, David Pflieger, Anders Bergström, Anastasie Sigwalt, Benjamin Barre, Kelle Freel, Agnès Llored, Corinne Cruaud, Karine Labadie, Jean-Marc Aury, Benjamin Istace, Kevin Lebrigand, Pascal Barbry, Stefan Engelen, Arnaud Lemainque, Patrick Wincker, Gianni Liti () and Joseph Schacherer ()
Additional contact information
Jackson Peter: Université de Strasbourg, CNRS, GMGM UMR 7156
Matteo De Chiara: Université Côte d’Azur, CNRS, INSERM, IRCAN
Anne Friedrich: Université de Strasbourg, CNRS, GMGM UMR 7156
Jia-Xing Yue: Université Côte d’Azur, CNRS, INSERM, IRCAN
David Pflieger: Université de Strasbourg, CNRS, GMGM UMR 7156
Anders Bergström: Université Côte d’Azur, CNRS, INSERM, IRCAN
Anastasie Sigwalt: Université de Strasbourg, CNRS, GMGM UMR 7156
Benjamin Barre: Université Côte d’Azur, CNRS, INSERM, IRCAN
Kelle Freel: Université de Strasbourg, CNRS, GMGM UMR 7156
Agnès Llored: Université Côte d’Azur, CNRS, INSERM, IRCAN
Corinne Cruaud: Commissariat à l’Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob
Karine Labadie: Commissariat à l’Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob
Jean-Marc Aury: Commissariat à l’Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob
Benjamin Istace: Commissariat à l’Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob
Kevin Lebrigand: Université Côte d’Azur, CNRS, IPMC
Pascal Barbry: Université Côte d’Azur, CNRS, IPMC
Stefan Engelen: Commissariat à l’Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob
Arnaud Lemainque: Commissariat à l’Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob
Patrick Wincker: Commissariat à l’Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob
Gianni Liti: Université Côte d’Azur, CNRS, INSERM, IRCAN
Joseph Schacherer: Université de Strasbourg, CNRS, GMGM UMR 7156

Nature, 2018, vol. 556, issue 7701, 339-344

Abstract: Abstract Large-scale population genomic surveys are essential to explore the phenotypic diversity of natural populations. Here we report the whole-genome sequencing and phenotyping of 1,011 Saccharomyces cerevisiae isolates, which together provide an accurate evolutionary picture of the genomic variants that shape the species-wide phenotypic landscape of this yeast. Genomic analyses support a single ‘out-of-China’ origin for this species, followed by several independent domestication events. Although domesticated isolates exhibit high variation in ploidy, aneuploidy and genome content, genome evolution in wild isolates is mainly driven by the accumulation of single nucleotide polymorphisms. A common feature is the extensive loss of heterozygosity, which represents an essential source of inter-individual variation in this mainly asexual species. Most of the single nucleotide polymorphisms, including experimentally identified functional polymorphisms, are present at very low frequencies. The largest numbers of variants identified by genome-wide association are copy-number changes, which have a greater phenotypic effect than do single nucleotide polymorphisms. This resource will guide future population genomics and genotype–phenotype studies in this classic model system.

Date: 2018
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DOI: 10.1038/s41586-018-0030-5

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