Exploring the genomic diversity of yeast involved in spontaneous fermentation: from studies to select autochthonous strains of different Italian wineries to extensive phylogenetic survey about the Italians’ population of s. cerevisiae

Modern winemakers must ensure effective alcoholic fermentation without losing the intrinsic biodiversity of the different oenological contexts. In this sense, the population of Saccharomyces cerevisiae characteristic of wineries that traditionally do not use selected yeasts can represent an interesting reservoir of biodiversity. The Edmund Mach Foundation began in the first decade of the 21st century a campaign of isolation, genotyping, and oenological evaluation of strains of S. cerevisiae in wineries of different Italian regions (Tuscany, Trentino, Alto Adige, Veneto). All the studies agreed in observing a high degree of biodiversity within the populations of S. cerevisiae, with traits specific to each winery, which led to distinguishing the yeasts based on their genetic and physiological traits, such as the resistance to wine limiting factors or the production of sensorially-active compounds. More recently, these results have stimulated an in-depth study that considers a large population of S. cerevisiae, coming from 24 Italian wineries. We have sequenced and studied the genome of both S. cerevisiae present in spontaneously fermented musts, by the set up a protocol based on polyphenols-removing prewashes, followed by both a whole-genome shotgun sequencing and the sequencing of selected S. cerevisiae clones to avoid the presence of artefactual chimaeras due to the copresence of strains. We reconstructed 45 genomes of S. cerevisiae strains for downstream functional analyses, and we performed an assembly-free metagenomic analysis to reconstruct the strain-level phylogeny of S. cerevisiae strains. This study will ensure the progress of knowledge about the ecology, evolution, and functional potential of the specie S. cerevisiae, as example the identification of reciprocal affinities of strains within the phylogeny of this specie, the degree of diversity of their genomes, and their impact on wine features, usually resumed in the concept of terroir.