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Genome evolution across 1,011 Saccharomyces cerevisiae isolates

Author

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  • 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
    CNRS UMR 8030, Université d’Evry Val d’Essonne)

  • Gianni Liti

    (Université Côte d’Azur, CNRS, INSERM, IRCAN)

  • Joseph Schacherer

    (Université de Strasbourg, CNRS, GMGM UMR 7156)

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.

Suggested Citation

  • 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, 2018. "Genome evolution across 1,011 Saccharomyces cerevisiae isolates," Nature, Nature, vol. 556(7701), pages 339-344, April.
    • Handle: RePEc:nat:nature:v:556:y:2018:i:7701:d:10.1038_s41586-018-0030-5
    DOI: 10.1038/s41586-018-0030-5
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    Cited by:

    1. Dariusz R. Kutyna & Cristobal A. Onetto & Thomas C. Williams & Hugh D. Goold & Ian T. Paulsen & Isak S. Pretorius & Daniel L. Johnson & Anthony R. Borneman, 2022. "Construction of a synthetic Saccharomyces cerevisiae pan-genome neo-chromosome," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    2. Abdullah Abdullatif Boudi & Abdulrahman Alshaikhmubarak, 2024. "Business Continuity and Sustainability in Government Organisations," Sustainability, MDPI, vol. 16(17), pages 1-19, August.
    3. Simone Mozzachiodi & Lorenzo Tattini & Agnes Llored & Agurtzane Irizar & Neža Škofljanc & Melania D’Angiolo & Matteo De Chiara & Benjamin P. Barré & Jia-Xing Yue & Angela Lutazi & Sophie Loeillet & Ra, 2021. "Aborting meiosis allows recombination in sterile diploid yeast hybrids," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    4. Vincent Somerville & Nadine Thierer & Remo S. Schmidt & Alexandra Roetschi & Lauriane Braillard & Monika Haueter & Hélène Berthoud & Noam Shani & Ueli Ah & Florent Mazel & Philipp Engel, 2024. "Genomic and phenotypic imprints of microbial domestication on cheese starter cultures," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    5. David Peris & Emily J. Ubbelohde & Meihua Christina Kuang & Jacek Kominek & Quinn K. Langdon & Marie Adams & Justin A. Koshalek & Amanda Beth Hulfachor & Dana A. Opulente & David J. Hall & Katie Hyma , 2023. "Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    6. Simone Mozzachiodi & Kristoffer Krogerus & Brian Gibson & Alain Nicolas & Gianni Liti, 2022. "Unlocking the functional potential of polyploid yeasts," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    7. Daniel Sultanov & Andreas Hochwagen, 2022. "Varying strength of selection contributes to the intragenomic diversity of rRNA genes," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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