Insights into the Dekkera bruxellensis genomic landscape: comparative genomics reveals variations in ploidy and nutrient utilisation potential amongst wine isolates

PLoS Genet. 2014 Feb 13;10(2):e1004161. doi: 10.1371/journal.pgen.1004161. eCollection 2014 Feb.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Australia
  • Biofuels / microbiology
  • Dekkera / genetics*
  • Dekkera / growth & development
  • Dekkera / metabolism
  • Fermentation
  • Genome*
  • Genomics
  • Phylogeny*
  • Ploidies
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Wine / microbiology*

Substances

  • Biofuels

Grant support

Research at the Australian Wine Research Institute is funded by Australia's grapegrowers and winemakers through their not-for-profit investment body, The Grape and Wine Research Development Corporation, with matching funding from the Australian government. Omics and Systems biology research at the AWRI uses resources provided as part of the National Collaborative Research Infrastructure Strategy (NCRIS), an initiative of the Australian Government, in addition to funds from the South Australian State Government. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.