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

Abstract

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.

Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis

“…Proteomes of A. robustus (NCBI taxid 1754,192), P. finnis (taxid 1754191), Neocallimastix californiae (1754190), Sch. japonicus (402676), D. bruxellensis (5007; [ 91 ]), K. marxianus (1003335) and O. parapolymorpha (871575) were subjected to protein blast search in NCBI [ 92 ], using LkUra1 (UniProt KB accession number Q7Z892) and LkUra9 (Q6V3W9) as queries and applying default settings. Similarly, the proteomes of A. robustus , P. finnis , N. californiae , Sch.…”

Microbial Dynamics between Yeasts and Acetic Acid Bacteria in Kombucha: Impacts on the Chemical Composition of the Beverage

“…They highlight, for the first time, the key role of yeasts and their metabolisms in terms of invertase activity and the fermentation capacity, which can differ, depending on yeast strains ( Table 1 ). Bibliographic resources and the NCBI database have reported the existence of genes encoding invertase in S. cerevisiae (internal and extracellular enzyme) [ 53 , 54 , 55 , 56 ] and B. bruxellensis (internal and extracellular enzyme) [ 57 , 58 , 59 , 60 ], but few data is available for H. valbyensis . However, genomic studies on the Hanseniaspora genus reported the loss of the SUC gene of the branch to which H. valbyensis belongs, thus supporting the low sucrose hydrolysis observed ( Table 1 ) [ 61 ].…”

Assessing Population Diversity of Brettanomyces Yeast Species and Identification of Strains for Brewing Applications

“…In its sexual form, it is also referred to as Dekkera, a genus comprising the most frequently found species Dekkera/Brettanomyces bruxellensis and Dekkera/Brettanomyces anomalus (for review, see Smith, 2011). In addition, other asexual species of Brettanomyces have been described, such as Brettanomyces naardenensis, Brettanomyces custersianus, and Brettanomyces nanus (Kurtzman et al, 2011;Tiukova et al, 2019;Roach and Borneman, 2020). The potential of Brettanomyces species for brewing is controversial, as it is usually recognized as a spoilage yeast, being the cause of major economic losses in many production facilities (Gilliland, 1961;Lebleux et al, 2020).…”