De novo Genome Assembly of a Native Saccharomyces cerevisiae Strain Isolated from Spontaneous Fermentation of Vineyard Must in the Atacama Desert (Chile)

Abstract

In this work, we investigated the genomic and phenotypic basis of stress tolerance in the native Saccharomyces cerevisiae strain M6, isolated from spontaneously fermenting must at a vineyard located in Atacama Desert, through a de novo hybrid genome assembly generated using short- and long-read sequencing technologies. The assembly comprised 11.89 Mb with high completeness (99.5%), and flow cytometry analysis confirmed a diploid genome organization. Phylogenomic analyses placed M6 within the Wine/European lineage, although displaying genomic divergence relative to other wine-associated strains. Using S288C as the reference genome, comparative variant analysis was performed for M6 and four closely related strains, including Wine/European and Alpechin strains. Coding variants were identified in genes associated with osmotic sensing and signaling (SSK1, SSK2), trehalose metabolism (TPS2, NTH1). Growth assays demonstrate that M6 exhibits enhanced performance under elevated temperatures (35–38°C) and high salinity (up to 1.5 M NaCl) compared with commercial and laboratory strains. In addition, Biolog YT assays revealed broad carbohydrate utilization capacity, including the metabolism of maltose, galactose, and raffinose-family oligosaccharides. Together, these results provide integrated genomic and phenotypic evidence of stress resistance and metabolic flexibility in strain M6, highlighting its potential as a biotechnological resource for fermentation processes.