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Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation

View ORCID ProfileJacob L. Steenwyk, View ORCID ProfileAntonis Rokas
doi: https://doi.org/10.1101/233122
Jacob L. Steenwyk
Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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Antonis Rokas
Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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  • ORCID record for Antonis Rokas
  • For correspondence: antonis.rokas@vanderbilt.edu
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Abstract

In recent years, copy number (CN) variation has emerged as a new and significant source of genetic polymorphisms contributing to the phenotypic diversity of populations. CN variants are defined as genetic loci that, due to duplication and deletion, vary in their number of copies across individuals in a population. CN variants range in size from 50 base pairs to whole chromosomes, can influence gene activity, and are associated with a wide range of phenotypes in diverse organisms, including the budding yeast Saccharomyces cerevisiae. In this review, we introduce CN variation, discuss the genetic and molecular mechanisms implicated in its generation, how they can contribute to genetic and phenotypic diversity in fungal populations, and consider how CN variants may influence wine yeast adaptation in fermentation-related processes. In particular, we focus on reviewing recent work investigating the contribution of changes in CN of fermentation-related genes associated with the adaptation and domestication of yeast wine strains and offer notable illustrations of such changes, including the high levels of CN variation among the CUP genes, which confer resistance to copper, and the preferential deletion and duplication of the MALI and MAL3 loci, respectively, which are responsible for metabolizing maltose and sucrose. Based on the available data, we propose that CN variation is a substantial dimension of yeast genetic diversity that occurs largely independent of single nucleotide polymorphisms. As such, CN variation harbors considerable potential for understanding and manipulating yeast strains in the wine fermentation environment and beyond.

  • Abbreviations

    BIR
    break-induced recombination
    CN
    copy number
    HR
    homologous recombination
    NHR
    non-homologous repair
    SNPs
    single nucleotide polymorphisms
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    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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    Posted December 12, 2017.
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    Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation
    Jacob L. Steenwyk, Antonis Rokas
    bioRxiv 233122; doi: https://doi.org/10.1101/233122
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    Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation
    Jacob L. Steenwyk, Antonis Rokas
    bioRxiv 233122; doi: https://doi.org/10.1101/233122

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