Draft genome sequence and transcriptome analysis of the wine spoilage yeastDekkera bruxellensisLAMAP2480 provides insights into genetic diversity, metabolism and survival

Abstract

Dekkera bruxellensis is the major contaminant yeast in the wine industry worldwide. Here, we present the draft genome sequence of D. bruxellensis LAMAP2480 isolated from a Chilean wine. Genomic evidence reveals shared and exclusive genes potentially involved in colonization and survival during alcoholic fermentation.

Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of <b><i>Brettanomyces bruxellensis</i></b> LAMAP2480

“…To date, the genome of 6 strains (AWRI1499 [Curtin et al, 2012], CBS2499 [Piškur et al, 2012], AWRI1608 and AWRI1613 [Borneman et al, 2014], ST05.12/22 [Crauwels et al, 2014], and LAMAP2480 [Valdes et al, 2014]) have been sequenced and annotated. All strains share food related traits, e.g., production of high ethanol levels and ability to grow in anaerobic conditions, similar to S. cerevisiae .…”

“…material). The genome statistics are similar to the first version of the B. bruxellensis LAMAP2480 genome [Valdes et al, 2014]; however, a more complete annotation was carried out. Additionally, read coverage and rates of polymorphism were computed based on alignments of Illumina transcriptome data (generated for polymorphism discovery) to the genome assembly.…”

“…The draft genome of the strain B. bruxellensis LAMAP2480 published by Valdes et al [2014] was reannotated using the GS de Novo Assembler [Margulies et al, 2005]. The sequenced reads (40× coverage) were used to reassemble the genome, yielding an assembly length of 27 Mb and N50 scaffold length of 5.5 kb (see online suppl.…”

“…We utilized all shotgun genomic sequence data (mate-pair libraries, bioproject: PRJNA231184) generated during B. bruxellensis LAMAP2480 sequencing [Valdes et al, 2014], carried out by 454 Life Sciences, Macrogen (Korea). It comprised samples of genomic DNA isolated using a standard zymolyase and phenol-chloroform extraction from cultures grown under standard conditions, from the Laboratory of Biotechnology and Applied Microbiological of the Universidad de Santiago de Chile.…”

“…Initially, efforts were dedicated to unravelling the genomic basis of its physiological properties, population dynamics, and the evolution of B. bruxellensis , which led to the generation of 6 draft genome sequences, B. bruxellensis CBS2499 [Piškur et al, 2012;Woolfit et al, 2007] and AWRI1499 [Curtin et al, 2012], AWRI1608 and AWRI1613 [Borneman et al, 2014], ST05.12/22 [Crauwels et al, 2014], and LAMAP2480 [Valdes et al, 2014] strains, obtaining the first genome blueprints of this species. Overall gene functional analysis has shown the presence of a large number of nitrogen transporters and lipids, some of which have not been described previously in other fermenting yeast such as S. cerevisiae .…”