Into the wild: new yeast genomes from natural environments and new tools for their analysis

• Published in: FEMS yeast research Vol. 20; no. 2; pp. 1 - 15
• Main Authors: Libkind, D, Peris, D, Cubillos, F A, Steenwyk, J L, Opulente, D A, Langdon, Q K, Rokas, A, Hittinger, C T
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.03.2020
• Subjects: Animal behavior; Ascomycota - genetics; BASIC BIOLOGICAL SCIENCES; Basidiomycota - genetics; Biotechnological microorganisms; Biotechnology; Chromosome Mapping; Computational Biology - methods; Domestication; Environment; Fermentation; Genome, Fungal; Genomes; Genomics; Hanseniaspora; Hanseniaspora - genetics; High-Throughput Nucleotide Sequencing; Microbial biotechnology; Mini Review; Minireview; Next-generation sequencing; Phaffia; Saccharomyces; Saccharomyces - genetics; Wild yeast; Wine - analysis; Yeast; Yeasts - classification; Yeasts - genetics; China; Phaffia; Hanseniaspora; Wild yeast; Biotechnology; Saccharomyces
• ISSN: 1567-1356; 1567-1364
• DOI: 10.1093/femsyr/foaa008

ABSTRACT Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts. New genome sequencing technologies together with new bioinformatic tools provide unique insights into the fascinating stories of wild and non-conventional yeast.