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Genomics and metabolomics of beer-spoiling yeast

The haploid S. cerevisiae strain S288C was the first eukaryotic organism to be fully sequenced in 1996 (Goffeau et al., 1996). Since this time, developments to next-generation sequencing have enabled the process to be undertaken cheaply and much more rapidly. Consequently, the genomes of over 40 different yeast species, including many capable of beer spoilage, have been published (Dujon, 2010). The vast majority of functional genomic studies in yeasts have focused on S. cerevisiae, largely due to the industrial applications of this species. However, with an increasing number of alternative sequences available for a variety of type strains and industrially significant yeasts, it is anticipated that the field of comparative genomics will develop significantly in the near future.

Currently, analysis has focused on the Sac- charomycetales yeasts, which include industrial strains and the majority of beer-spoiling species, including B. bruxellensis, C. tropicalis, D. hansenii, K. lactis, K. marxianus, P. guilliermondii, Sch. pombe

and Z. Rouxii. All of these organisms are relatively closely related (Fig. 11.5) and have genomes that range in size from 9 to 20 Mb (for haploids) and contain =4700-6500 protein-coding genes located on between 4 and 16 chromosomes (Dujon, 2010). Chromosome number is highly variable between species and sometimes between strains, while there is also strong evidence to suggest that heterospecific hybridization between yeasts is relatively common. Interestingly, all of the yeast genomes analysed to date appear to contain a large number of paralogous gene copies, i.e. genes with shared ancestry due to duplication events. In beer-spoiling organisms, this may either impact on how ‘robust' strains are, since gene duplications

offer a degree of genetic and evolutionary plasticity (Gu et al., 2003), or expand functionality due to overlapping metabolic roles (Kuepfer et al., 2005). Analysis of gene variation between species indicates that there is a trend towards expansion of tandem gene arrays. This is significant from a beer- spoiling perspective since genes known to impact on flocculation contain highly repeated sequences that influence the ‘strength' of flocculation (Ver- strepen et al., 2005). Similarly, repeat elements are associated with the CUP1 gene (Zhao et al., 2014), which dictates copper resistance, one of the major means of differentiating between culture yeast and non-Saccharomyces strains (see section ‘Detection and identification', below). Finally, there is also

Phylogenetic tree of beer-spoiling yeasts, providing an indication of the evolutionary relationship between species based on a variety of DNA analyses

Figure 11.5 Phylogenetic tree of beer-spoiling yeasts, providing an indication of the evolutionary relationship between species based on a variety of DNA analyses (see Suh et al., 2006; Kurtzman et al., 2008; Kurtzman and Robnett, 2013, for more details). Branch lengths are not indicative of evolutionary distance. Note that although Brettanomyces is often described as being a member of the Pichiaceae family, this assignment is uncertain. According to certain measures of analysis, Brettanomyces and other Pichiaceae yeasts are only distantly related (Kurtzman and Boekhout, 2011), hence it is placed separately here.

evidence of horizontal gene transfer from bacterial species in certain yeasts and the presence of autonomous plasmids or viral elements that could have a significant impact on both the functionality and the threat to industrial fermentation systems (Keeling and Palmer, 2008; Coelho et al., 2013; Lacroix and Citovsky, 2016). When comparing the genomic impact of production brewing strains and beer-spoiling yeasts directly, there are also some more obvious differences that have a major influence on spoilage potential. These are related to flavour development, flocculation, killer activity, and general metabolic activity as described below.

 
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