High complexity and degree of genetic variation inBrettanomyces bruxellensispopulation

Abstract

<jats:title>Abstract</jats:title><jats:p>Genome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype-phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, <jats:italic>Saccharomyces cerevisiae</jats:italic> and <jats:italic>Schizosaccharomyces pombe</jats:italic>. In this context, we sought to explore an uncharacterized yeast species, <jats:italic>Brettanomyces bruxellensis</jats:italic>, which is a major cause of wine spoilage but also can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 <jats:italic>B. bruxellensis</jats:italic> strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the <jats:italic>B. bruxellensis</jats:italic> species. Genomes are punctuated by multiple loss-of-heterozygosity regions while aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared to <jats:italic>S. cerevisiae</jats:italic>. The pangenome is composed of 4,923 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.</jats:p>

Different trajectories of polyploidization shape the genomic landscape of theBrettanomyces bruxellensisyeast species

“…Using this dataset, we sampled 24,313 genetic variants evenly distributed across the genome and performed a phylogenetic analysis (Figure 1B). All the 71 strains were clustered into six well-defined lineages, which correlate with environmental niche, as previously reported (Avramova et al 2018, Gounot et al 2020, Colomer et al 2020). We then assigned ploidy state to each of the strains using SNP frequency distributions within the sequence reads.…”

“…Brettanomyces bruxellensis is known as a diverse species with genetically and ecologically distinct clusters, and various levels of ploidy (Avramova et al 2018, Gounot et al 2020, Colomer et al 2020). To dissect the genomic architecture and to further understand the origin as well as the trajectories of recently described polyploid groups, we selected 71 strains with 51 coming from subpopulations defined as polyploids (Avramova et al 2018) (Figure 1A; Supplementary Table S1).…”

“…To justify the conserved pattern per group from an adaptive evolutionary perspective, we checked if the regions, either gained or lost from the primary genome, are enriched for genes with particular functions. We used the genome annotation from Gounot et al (2020) and checked for Gene-Ontology (GO) terms in regions that have gained or lost a copy of the primary genome. Additionally, we checked regions that are different in ploidy between the beer and the wine 1 subpopulation.…”

Assessing Population Diversity of Brettanomyces Yeast Species and Identification of Strains for Brewing Applications

“…To date, several assemblies of B. bruxellensis species have been published (Curtin et al, 2012;Piškur et al, 2012;Borneman et al, 2014;Crauwels et al, 2014;Olsen et al, 2015;Fournier et al, 2017) displaying a wide intra-specific variability of B. bruxellensis species (Woolfit et al, 2007;Hellborg and Piškur, 2009;Borneman et al, 2014). There are frequent variations at genomic level, including re-organizations and gene duplications, with the number of chromosomes varying from 4 to 9 (Woolfit et al, 2007;Gounot et al, 2019). While most of the population is diploid (2n) or triploid (3n) (Borneman et al, 2014;Avramova et al, 2018a), up to five alleles for certain locus have been reported (Avramova et al, 2018a).…”

+Brettanomyces bruxellensis Displays Variable Susceptibility to Chitosan Treatment in Wine

“…This is particularly true for B. bruxellensis , the main microbial target of chitosan treatment in wine. B. bruxellensis gathers triploid and diploid strains distributed in at least six main genetic groups ( Avramova et al, 2018a ; Gounot et al, 2020 ). Wine isolates are also highly diverse and belong to 5 of these genetic groups ( Cibrario et al, 2019 ).…”