Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines.
Bottom Line: A study on the orthologs and single nucleotide polymorphism contents of the genetic groups revealed that the domestication of some strains to products such as cider, wine, or champagne, is reflected at the genetic level.While group A strains proved to be predominant in wine and to form subgroups adapted to specific types of wine such as champagne, group B strains were found in wine and cider.The results suggest that ancestral O. oeni strains were adapted to low-ethanol containing environments such as overripe fruits, and that they were domesticated to cider and wine, with group A strains being naturally selected in a process of further domestication to specific wines such as champagne.
Affiliation: Univ. Bordeaux, ISVV, EA 4577 Œnologie, Villenave d'Ornon, France Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.Show MeSH
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Mentions: Raw reads were mapped against the reference genome of strain PSU-1 with the program BWA bwasw (Li and Durbin 2010). Single nucleotide polymorphism (SNP) were extracted with SAMtools and BCFtools (Li et al. 2009). An independent mapping and extraction of the SNP was carried out with MUMmer nucmer (Kurtz et al. 2004), both for the already assembled public genomes and for the final assemblies of the genomes of this study. The 47,621 resulting SNP positions were parsed into a matrix containing the allele carried by each strain. The distribution of SNP among different groups of strains was determined by measuring the Shannon Entropy for each SNP with the formula H = −∑p(xi) log2p(xi), where p(xi) represents the probability of finding the allele xi in an arbitrarily defined group of strains. The entropy was calculated for the groups of strains “A,”” B,” “strain IOEB_C52,” “champagne,” and “cider” as defined in figure 2. A SNP was considered to be unique to a certain group of strains whenever its entropy (H) was equal to 0 for the given group. The effect of each SNP was analyzed by snpEff (Cingolani et al. 2012), using the public genome of PSU-1 as reference. SNP affecting noncoding zones were discarded for the snpEff analysis.
Affiliation: Univ. Bordeaux, ISVV, EA 4577 Œnologie, Villenave d'Ornon, France Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.