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.
Highlights
Dekkera (Brettanomyces) bruxellensis has been described in the population ecology of various fermented beverages, such as wine, beer and cider [1,2,3], and is of increasing relevance to the biofuel industry [4]
Unlike S. cerevisiae, D. bruxellensis is highly intractable in the laboratory; it is difficult to mate and to transform, making even the most basic genetic analysis very difficult
The current manuscript describes a comparative genomics approach to providing insights into inter-strain variations that shape the genomic landscape of D. bruxellensis
Summary
Dekkera (Brettanomyces) bruxellensis has been described in the population ecology of various fermented beverages, such as wine, beer and cider [1,2,3], and is of increasing relevance to the biofuel industry [4]. One third of D. bruxellensis isolates from a range of sources do not grow on nitrate as a sole nitrogen source [8]; presumably nitrate assimilation is less important for D. bruxellensis in some fermentation ecosystems. In another recent study, variation in sulphite tolerance in D. bruxellensis was linked to amplified fragment length polymorphism (AFLP) and 26S rDNA genetic markers [11], inferring a genetic basis for previously reported regional variation and groupings of this yeast across Australian wineries [1]
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