Abstract
BackgroundSaccharomycodes ludwigii belongs to the poorly characterized Saccharomycodeacea family and is known by its ability to spoil wines, a trait mostly attributable to its high tolerance to sulfur dioxide (SO2). To improve knowledge about Saccharomycodeacea our group determined whole-genome sequences of Hanseniaspora guilliermondii (UTAD222) and S. ludwigii (UTAD17), two members of this family. While in the case of H. guilliermondii the genomic information elucidated crucial aspects concerning the physiology of this species in the context of wine fermentation, the draft sequence obtained for S. ludwigii was distributed by more than 1000 contigs complicating extraction of biologically relevant information. In this work we describe the results obtained upon resequencing of S. ludwigii UTAD17 genome using PacBio as well as the insights gathered from the exploration of the annotation performed over the assembled genome.ResultsResequencing of S. ludwigii UTAD17 genome with PacBio resulted in 20 contigs totaling 13 Mb of assembled DNA and corresponding to 95% of the DNA harbored by this strain. Annotation of the assembled UTAD17 genome predicts 4644 protein-encoding genes. Comparative analysis of the predicted S. ludwigii ORFeome with those encoded by other Saccharomycodeacea led to the identification of 213 proteins only found in this species. Among these were six enzymes required for catabolism of N-acetylglucosamine, four cell wall β-mannosyltransferases, several flocculins and three acetoin reductases. Different from its sister Hanseniaspora species, neoglucogenesis, glyoxylate cycle and thiamine biosynthetic pathways are functional in S. ludwigii. Four efflux pumps similar to the Ssu1 sulfite exporter, as well as robust orthologues for 65% of the S. cerevisiae SO2-tolerance genes, were identified in S. ludwigii genome.ConclusionsThis work provides the first genome-wide picture of a S. ludwigii strain representing a step forward for a better understanding of the physiology and genetics of this species and of the Saccharomycodeacea family. The release of this genomic sequence and of the information extracted from it can contribute to guide the design of better wine preservation strategies to counteract spoilage prompted by S. ludwigii. It will also accelerate the exploration of this species as a cell factory, specially in production of fermented beverages where the use of Non-Saccharomyces species (including spoilage species) is booming.
Highlights
Saccharomycodes ludwigii belongs to the poorly characterized Saccharomycodeacea family and is known by its ability to spoil wines, a trait mostly attributable to its high tolerance to sulfur dioxide (SO2)
While S. ludwigii is still seen as a spoilage species, the presence of H. guilliermondii and H. uvarum has recently been considered positive because these species improve wine aromatic properties by producing aroma compounds that are not produced by S. cerevisiae, the species that leads vinification [3, 4]
The results obtained revealed seven clearly separated chromosomal bands, ranging from 0.9 Mbp to 2.9 Mb, totaling 13.75 Mbp (Fig. 1). This number of chromosomes and their size range is consistent with what was previously described for other S. ludwigii strains [30] and is in line with what is reported for other members of the Saccharomycodeacea family [31,32,33]
Summary
Saccharomycodes ludwigii belongs to the poorly characterized Saccharomycodeacea family and is known by its ability to spoil wines, a trait mostly attributable to its high tolerance to sulfur dioxide (SO2). The identification of S. ludwigii in plant fluids [8, 11] as well as in the intestinal microbiota of insects found in vineyards [12, 13], led to the hypothesis that these yeasts could be transported from trees to grapes and/or to cellar equipments. This issue, still requires further clarification as more information about the species are gathered. S. ludwigii strains have been isolated from other sources such as spoiled carbonated beverages [15], fermented fruit juices [16, 17] or beverages with high ethanol such as mezcal or tequila [18]
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