Extensive Copy Number Variation in Fermentation-Related Genes amongSaccharomyces cerevisiaeWine Strains

Abstract

Due to the importance of Saccharomyces cerevisiae in 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 of S. cerevisiae wine 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 the SNO gene 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.

New genome assemblies reveal patterns of domestication and adaptation across Brettanomyces (Dekkera) species

“…The genomic context illustrates further parallels to evolution in Saccharomyces. The invertases are shown to reside within sub-telomeres, which are genomic regions that have been shown to be hotspots for structural rearrangements and HGT events in Saccharomyces [59][60][61][62][63]. Sucrose utilization likely conferred a significant advantage in fruit fermentations, helping to shape the evolution of the common ancestor of B. bruxellensis and B. anomalus towards this fermentation specialization.…”

Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina

“…In addition to the analysis of gene expression, single nucleotide polymorphisms (SNPs), and insertions/deletions (InDels) [ 21 , 23 , 27 , 28 ], copy number variations (CNVs) have been highlighted as a new and significant source of genetic polymorphism that contributes to phenotypic diversity such as virulence in diverse fungal species [ 29 ]. In fact, the contribution of CNVs to population genetic and phenotypic diversity has been exemplified by a range of fungal studies, including studies on yeast Saccharomyces cerevisiae (Ascomycota, Saccharomycetes) [ 30 , 31 ], the wheat pathogen Zymoseptoria tritici (Ascomycota, Dothideomycetes) [ 32 ], and the human fungal pathogen Cryptococcus deuterogattii (Basidiomycota, Tremellomycetes) [ 33 ]. It has also been noted that the degree of CNV in fungal populations is not always correlated with the degree of SNP variation, which indicated that CNV analysis could reveal an important yet hidden layer of genetic information independent of SNPs/InDels.…”

Many interspecific chromosomal introgressions are highly prevalent in Holarctic Saccharomyces uvarum strains found in human‐related fermentations

“…Saccharomyces uvarum is a striking example of a yeast species whose genome is strongly shaped by introgressed regions (Almeida et al, ). S. uvarum shares partially overlapping ecological niches with S. cerevisiae : both are strongly related to human‐driven fermentation, but S. uvarum is more psychrotrophic and thus is more frequently associated with low‐temperature processes: cider‐making and winemaking in northern – cooler – French vineyards for example (Masneuf‐Pomarede et al, ; Tosi et al, ; Demuyter et al, ; Naumov et al, ). Isolates from natural environments (insect, plant, soil) have also been described (Sampaio & Gonçalves, ; Boynton & Greig, ).…”