New genome assemblies reveal patterns of domestication and adaptation acrossBrettanomyces(Dekkera) species

Abstract

Background. Yeast of the genus Brettanomyces are of significant interest, both for their capacity to spoil, as well as their potential to positively contribute to different industrial fermentations. However, considerable variance exists in the depth of research and knowledgebase of the five currently known species of Brettanomyces. For instance, Brettanomyces bruxellensis has been heavily studied and many resources are available for this species, whereas Brettanomyces nanus is rarely studied and lacks a publicly available genome assembly altogether. The purpose of this study is to fill this knowledge gap and explore the genomic adaptations that have shaped the evolution of this genus. Results. Strains for each of the five widely accepted species of Brettanomyces (Brettanomyces anomalus, B. bruxellensis, Brettanomyces custersianus, Brettanomyces naardenensis, and B. nanus) were sequenced using a combination of long-and short-read sequencing technologies. Highly contiguous assemblies were produced for each species. Sweeping and extensive structural variation between the species' genomes were observed and gene expansions in fermentation-relevant genes (particularly in B. bruxellensis and B. nanus) were identified. Numerous horizontal gene transfer (HGT) events in all Brettanomyces species', including an HGT event that is probably responsible for allowing B. bruxellensis and B. anomalus to utilize sucrose were also observed. Conclusions. Genomic adaptations and some evidence of domestication that have taken place in Brettanomycesare outlined. These new genome assemblies form a valuable resource for future research in Brettanomyces.