title: Extensive Copy Number Variation in Fermentation-Related Genes AmongSaccharomyces cerevisiaeWine Strains.
abstract: Due to the importance ofSaccharomyces cerevisiaein wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences ofS. cerevisiaewine strains. We found an average of 97.8 CN variable regions (CNVRs) affecting ∼4% of the genome per strain. Using two different measures of CN diversity, we found that gene families involved in fermentation-related processes such as copper resistance (CUP), flocculation (FLO), and glucose metabolism (HXT), as well as theSNOgene family whose members are expressed before or during the diauxic shift, showed substantial CN diversity across the 132 strains examined. Importantly, these same gene families have been shown, through comparative transcriptomic and functional assays, to be associated with adaptation to the wine fermentation environment. Our results suggest that CN variation is a substantial contributor to the genomic diversity of wine yeast strains, and identify several candidate loci whose levels of CN variation may affect the adaptation and performance of wine yeast strains during fermentation.
authors.affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235.
authors.forename: Jacob
authors.identifier: 0000-0002-8436-595X
authors.initials: J
authors.lastname: Steenwyk
authors.affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235 antonis.rokas@vanderbilt.edu.
authors.forename: Antonis
authors.identifier: 0000-0002-7248-6551
authors.initials: A
authors.lastname: Rokas
mesh_terms: D056915:DNA Copy Number Variations; D005285:Fermentation / Q000235:genetics*; D005800:Genes, Fungal; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D014920:Wine / Q000382:microbiology
keywords: alcoholic fermentation; carbohydrate metabolism; domestication; genomics; structural variation