Large-scale sequencing and comparative analysis of oenological Saccharomyces cerevisiae strains supported by nanopore refinement of key genomes. (August 2021)

• Record Type: Journal Article
• Authors: Basile, Arianna; De Pascale, Fabio; Bianca, Federico; Rossi, Alessandro; Frizzarin, Martina; De Bernardini, Nicola; Bosaro, Matteo; Baldisseri, Anna; Antoniali, Paolo; Lopreiato, Raffaele; Treu, Laura; Campanaro, Stefano
• Is Part Of: Food microbiology. Volume 97(2021)
• Publication Date: 2021-08
• Subjects: Saccharomyces cerevisiae -- Oenological strains -- Winemaking -- Genomic variants -- SNP -- Comparative genomics; Food Microbiology -- Periodicals; Aliments -- Microbiologie -- Périodiques; Food -- Microbiology; Periodicals; Food -- Microbiology -- Periodicals; Food contamination -- Periodicals; 664.001579
• DOI: 10.1016/j.fm.2021.103753
• Languages: English
• ISSNs: 0740-0020

Abstract

Abstract: Saccharomyces cerevisiae has long been part of human activities related to the production of food and wine. The industrial demand for fermented beverages with well-defined and stable characteristics boosted the isolation and selection of strains conferring a distinctive aroma profile to the final product. To uncover variants characterizing oenological strains, the sequencing of 65 new S. cerevisiae isolates, and the comparison with other 503 publicly available genomes were performed. A hybrid approach based on short Illumina and long Oxford Nanopore reads allowed the in-depth investigation of eleven genomes and the identification of putative laterally transferred regions and structural variants. A comparative analysis between clusters of strains belonging to different datasets allowed the identification of novel relevant genetic features including single nucleotide polymorphisms, insertions and structural variants. Detection of oenological single nucleotide variants shed light on the existence of different levels of modulation for the mevalonate pathway relevant for the biosynthesis of aromatic compounds. Highlights: Illumina sequencing of 65 new Saccharomyces cerevisiae oenological strains. Oxford Nanopore long reads generated a high-quality assembly of eleven strains. A SNPs-based tree showed the phylogenetic clustering of 455 oenological strains. Resistance to chemical stresses was determined by structural variants and CNVs. Variants with high phenotypic impact influence sulfate and glycerol production.