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: To evaluate whether the pangenome (sum of all the genes of all the collected strains) (Medini et al. 2005; Tettelin et al. 2008) of the species has been fully represented, we determined the ortholog groups, analyzed the composition of the pangenome, and plotted the evolution of the coregenome (set of genes shared by all the strains) versus the pangenome from 1 to 50 strains (fig. 1). Tendency of the curves suggests that neither the coregenome nor the pangenome of the species has been fully represented yet. The pangenome for the 50 strains is represented by 3,235 CDS, distributed in 2,469 ortholog groups (table 2). The core genome is represented by 1,368 CDS, distributed in 1,160 orthologs. There are also 1,452 CDS that form the shellgenome (genes shared by only some strains) distributed in 902 ortholog groups, whereas 415 CDS belong to the cloud genome (genes present in only one strain). The size of the pangenome is consistent with previous studies that showed a pangenome size of 2,846 CDS for a group of 14 strains (Borneman et al. 2012a). However, the size of the coregenome is bigger than that of the fore mentioned study (1,165 CDS for the group of 14 strains), a divergence that is due to the different methods used to determine orthologs. Due to this divergence of the methods, if we recalculate the pan and coregenomes for the group of 14 strains we get a set of 2,639 and 1,512 genes, respectively.Fig. 1.—
Affiliation: Univ. Bordeaux, ISVV, EA 4577 Œnologie, Villenave d'Ornon, France Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.