Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis

Abstract

The hemiascomycete yeast Dekkera bruxellensis, also known as Brettanomyces bruxellensis, is a major cause of wine spoilage worldwide. Wines infected with D. bruxellensis develop distinctive, unpleasant aromas due to volatile phenols produced by this species, which is highly ethanol tolerant and facultatively anaerobic. Despite its importance, however, D. bruxellensis has been poorly genetically characterized until now. We performed genome survey sequencing of a wine strain of D. bruxellensis to obtain 0.4x coverage of the genome. We identified approximately 3,000 genes, whose products averaged 49% amino acid identity to their Saccharomyces cerevisiae orthologs, with similar intron contents. Maximum likelihood phylogenetic analyses suggest that the relationship between D. bruxellensis, S. cerevisiae, and Candida albicans is close to a trichotomy. The estimated rate of chromosomal rearrangement in D. bruxellensis is slower than that calculated for C. albicans, while its rate of amino acid evolution is somewhat higher. The proteome of D. bruxellensis is enriched for transporters and genes involved in nitrogen and lipid metabolism, among other functions, which may reflect adaptations to its low-nutrient, high-ethanol niche. We also identified an adenyl deaminase gene that has high similarity to a gene in bacteria of the Burkholderia cepacia species complex and appears to be the result of horizontal gene transfer. These data provide a resource for further analyses of the population genetics and evolution of D. bruxellensis and of the genetic bases of its physiological capabilities.

FIG. 1.

(A) Consensus network based on 396 protein trees; splits are shown if they are present in 25% or more of the trees. Three incompatible splits involving the placement of D. bruxellensis generate a cube in the network. (B to D) Three likely topologies inferred from the consensus network. Each topology contains one of the incompatible splits shown in panel A; in each case the branch corresponding to the split is marked with an asterisk. Branch lengths for these three trees are estimated by maximum likelihood using concatenated amino acid sequence data.

FIG. 2.

Distribution of GC content at third-position codon sites in 2,606 orthologous genes in D. bruxellensis and S. cerevisiae.

FIG. 3.

Estimated rates of chromosomal rearrangements between D. bruxellensis, C. albicans, and S. cerevisiae. Black arrows indicate analyses performed in this study, while the white arrow refers to a previous study (55). The percentage of adjacent gene pairs conserved between species was calculated from the data, and the percentage of gene pair adjacencies disrupted by gene loss following whole genome duplication (WGD) in S. cerevisiae is estimated to be approximately equal to the percentage conserved. The remaining gene pairs have been disrupted by chromosomal rearrangements.

FIG. 4.

(A) Gene order relationships (not drawn to scale) of five nitrate assimilation genes and their neighboring genes in the D. bruxellensis data. See Table 2 for full gene names. The arrowheads indicate the direction of transcription. Solid lines between genes indicate sequenced intergenic regions; dotted lines indicate that the gene order is inferred from clone end pair information. (B) Order and orientation of the cluster of orthologous genes in Hansenula polymorpha (based on information provided in reference 4).

FIG. 5.

Maximum likelihood phylogenetic tree, based on amino acid sequences, showing the relationships between adenine deaminases (ADEs, green), adenosine deaminases (ADAs, blue), and the cluster of horizontally transferred genes (red). Bootstrap values (1,000 replicates) are given for branches of interest. GenBank accession numbers are given in parentheses for Burkholderia genes.