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Background  Yeasts 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. Structural differences between the species’ genomes were observed with gene expansions in fermentation-relevant genes (particularly in  B. bruxellensis  and  B. nanus ) 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  Brettanomyces  are outlined. These new genome assemblies form a valuable resource for future research in  Brettanomyces .

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