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 in 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, a metal with fungicidal properties, and the preferential deletion and duplication of the MAL1 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.
Highlights
Genetic variation in natural populations is shaped by diverse biological processes, such as genetic drift and natural selection (Chakravarti, 1999), and is, in part, responsible for phenotypic variation
In S. cerevisiae, copy number (CN) variants have been shown to influence ecologically-relevant phenotypes; CUP1 duplications have been repeatedly associated with resistance to copper (Fogel and Welch, 1982; Strope et al, 2015) and duplications in the MAL loci, which facilitate the utilization of maltose, the main carbon source during beer fermentation and present in sake fermentations, are frequently observed among beer and sake yeast strains, (Vidgren et al, 2005; Gallone et al, 2016; Gonçalves et al, 2016)
An emerging body of work suggests that CN variation is an important, largely underappreciated, dimension of fungal genome biology and evolution (Hu et al, 2011; Farrer et al, 2013; Gallone et al, 2016; Gonçalves et al, 2016; Steenwyk et al, 2016; Hartmann and Croll, 2017; Steenwyk and Rokas, 2017)
Summary
Genetic variation in natural populations is shaped by diverse biological processes, such as genetic drift and natural selection (Chakravarti, 1999), and is, in part, responsible for phenotypic variation. Interrogations of genome-wide patterns of SNPs have shown that industrial lineages – including those of beer, bread, cacao, sake, and wine – often mirror human history (Schacherer et al, 2009; Sicard and Legras, 2011; Cromie et al, 2013; Gallone et al, 2016; Gonçalves et al, 2016), suggesting that human activity has greatly influenced S. cerevisiae genome evolution (Yue et al, 2017). SNP-based studies have repeatedly found that wine strains of S. cerevisiae exhibit low levels of genetic diversity (Liti et al, 2009; Schacherer et al, 2009; Sicard and Legras, 2011; Cromie et al, 2013; Borneman et al, 2016), consistent with a historical population bottleneck event that reduced wine yeast genetic variation. We begin by surveying the molecular mechanisms that lead to CN variant formation, we discuss the contribution of CN variation to the genetic and phenotypic diversity in fungal populations, and close by examining the CN variation in wine yeasts and the likely phenotypic impact of CN variants in the wine fermentation environment
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