Insights into the Dekkera bruxellensis Genomic Landscape: Comparative Genomics Reveals Variations in Ploidy and Nutrient Utilisation Potential amongst Wine Isolates

Abstract

The yeast Dekkera bruxellensis is a major contaminant of industrial fermentations, such as those used for the production of biofuel and wine, where it outlasts and, under some conditions, outcompetes the major industrial yeast Saccharomyces cerevisiae. In order to investigate the level of inter-strain variation that is present within this economically important species, the genomes of four diverse D. bruxellensis isolates were compared. While each of the four strains was shown to contain a core diploid genome, which is clearly sufficient for survival, two of the four isolates have a third haploid complement of chromosomes. The sequences of these additional haploid genomes were both highly divergent from those comprising the diploid core and divergent between the two triploid strains. Similar to examples in the Saccharomyces spp. clade, where some allotriploids have arisen on the basis of enhanced ability to survive a range of environmental conditions, it is likely these strains are products of two independent hybridisation events that may have involved multiple species or distinct sub-species of Dekkera. Interestingly these triploid strains represent the vast majority (92%) of isolates from across the Australian wine industry, suggesting that the additional set of chromosomes may confer a selective advantage in winery environments that has resulted in these hybrid strains all-but replacing their diploid counterparts in Australian winery settings. In addition to the apparent inter-specific hybridisation events, chromosomal aberrations such as strain-specific insertions and deletions and loss-of-heterozygosity by gene conversion were also commonplace. While these events are likely to have affected many phenotypes across these strains, we have been able to link a specific deletion to the inability to utilise nitrate by some strains of D. bruxellensis, a phenotype that may have direct impacts in the ability for these strains to compete with S. cerevisiae.

Assessing Genetic Diversity among Brettanomyces Yeasts by DNA Fingerprinting and Whole-Genome Sequencing

“…Given the triploid nature of AWRI 1499, comprising a moderately heterozygous diploid and a third divergent haploid (24,34), and the fact that CBS 2499 was recently confirmed to be a diploid (34), it was of interest to investigate the genomic organization of our strain in relation to that of both reference strains. First, the ploidy level of ST05.12/22 was estimated by taking advantage of allele proportions.…”

“…4, ST05.12/22 showed a maximum average allele frequency consistent with a diploid state, suggesting that ST05.12/22 is diploid. In order to determine whether the diploid strains contained the divergent haplotype of AWRI 1499, five loci that displayed three clearly defined haplotypes in AWRI 1499 (24,34) were investigated. Maximum likelihood phylogenies were constructed on the basis of the corresponding individual haplotype sequences for AWRI 1499 (3 sequences for each locus), CBS 2499 (2 sequences for each locus), and ST05.12/22 (2 sequences for each locus).…”

“…Comparative genomics of four wine isolates, including CBS 2499, AWRI 1499, and two newly sequenced B. bruxellensis isolates, revealed differences in nutrient utilization and ploidy level within B. bruxellensis, with some strains being diploid and others being triploid (34). Triploid isolates were found to possess a core diploid genome and a distantly related third genomic complement (34).…”

“…Triploid isolates were found to possess a core diploid genome and a distantly related third genomic complement (34). Further, the authors presented evidence suggesting that this form of triploidy has arisen more than once in the evolutionary history of B. bruxellensis and that it confers a selective advantage for strains from wineries (34).…”

“…Triploid isolates were found to possess a core diploid genome and a distantly related third genomic complement (34). Further, the authors presented evidence suggesting that this form of triploidy has arisen more than once in the evolutionary history of B. bruxellensis and that it confers a selective advantage for strains from wineries (34). Whereas the sequencing of these wine spoilage B. bruxellensis strains has increased our understanding of this species, our knowledge of how these strains behave in comparison with strains from another niche remains fairly limited.…”