Whole-Genome Analysis of Three Yeast Strains Used for Production of Sherry-Like Wines Revealed Genetic Traits Specific to Flor Yeasts

Abstract

Flor yeast strains represent a specialized group of Saccharomyces cerevisiae yeasts used for biological wine aging. We have sequenced the genomes of three flor strains originated from different geographic regions and used for production of sherry-like wines in Russia. According to the obtained phylogeny of 118 yeast strains, flor strains form very tight cluster adjacent to the main wine clade. SNP analysis versus available genomes of wine and flor strains revealed 2,270 genetic variants in 1,337 loci specific to flor strains. Gene ontology analysis in combination with gene content evaluation revealed a complex landscape of possibly adaptive genetic changes in flor yeast, related to genes associated with cell morphology, mitotic cell cycle, ion homeostasis, DNA repair, carbohydrate metabolism, lipid metabolism, and cell wall biogenesis. Pangenomic analysis discovered the presence of several well-known “non-reference” loci of potential industrial importance. Events of gene loss included deletions of asparaginase genes, maltose utilization locus, and FRE-FIT locus involved in iron transport. The latter in combination with a flor-yeast-specific mutation in the Aft1 transcription factor gene is likely to be responsible for the discovered phenotype of increased iron sensitivity and improved iron uptake of analyzed strains. Expansion of the coding region of the FLO11 flocullin gene and alteration of the balance between members of the FLO gene family are likely to positively affect the well-known propensity of flor strains for velum formation. Our study provides new insights in the nature of genetic variation in flor yeast strains and demonstrates that different adaptive properties of flor yeast strains could have evolved through different mechanisms of genetic variation.

Transcriptome Profile of Yeast Strain Used for Biological Wine Aging Revealed Dynamic Changes of Gene Expression in Course of Flor Development

“…Six to nine million of 50-bp single-end reads were generated for each sample. The previously assembled genome of S. cerevisiae strain I-329 (GenBank PTER00000000, Eldarov et al, 2018) was used as a reference for the expression analysis.…”

“…To gain insight into the dynamics of transcriptional responses of industrial flor yeast strain at stage of biofilm formation we used the previously sequenced flor strain I-329 (Eldarov et al, 2018). This strain was chosen because it is used for industrial production of sherry-like wine in Russia, it is tolerant to high ethanol concentration (16-17%) and could retain high viability at the biofilm stage (Kishkovskaia et al, 2017).…”

“…Previous taxonomic and comparative genomic studies of wine and flor yeast strains showed that flor yeasts form a separate phylogenetic group artificially selected in the course of domestication and possessing unique physiological and genetic properties (Legras et al, 2014;Coi et al, 2017;Eldarov et al, 2018). Genome-wide comparative analysis of wine and flor strains revealed 2270 flor-yeast specific SNPs located in 1337 loci (Eldarov et al, 2018) with 73 SNP located in intergenic regions and the rest in 1334 protein-coding genes. Transcriptome analysis of these genes revealed 369 DEGs (27.7%) with more than 2-fold alterations in expression levels, 188 upregulated and 181 downregulated ( Table 2).…”

“…Recent extensive comparative genomic analysis supports and extends this view. Comparison of wine and flor yeast genomes have revealed a complex landscape of genetic variation specific for flor yeast including hundreds of SNPs, InDels, chromosomal rearrangements, gene content alterations (Coi et al, 2017;Eldarov et al, 2018;Legras et al, 2018). Many of these structural variations have affected key regulatory molecules (transcription factors, signal transduction molecules), suggesting direct influence on gene expression patterns of target genes, involved in metabolic and morphological changes specific for flor yeast (Coi et al, 2017;Eldarov et al, 2018).…”

“…Here, we report a comprehensive transcriptome analysis of flor yeast gene expression using RNA-seq data. We generated transcriptomic data for a recently sequenced flor yeast strain I-329, for which detailed microbiological, biochemical, physiological data is also available (Kishkovskaia et al, 2017;Eldarov et al, 2018). This strain was grown under conditions mimicking biological wine aging, at three consecutive stages of velum formation and growth.…”