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Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines.

Campbell-Sills H, El Khoury M, Favier M, Romano A, Biasioli F, Spano G, Sherman DJ, Bouchez O, Coton E, Coton M, Okada S, Tanaka N, Dols-Lafargue M, Lucas PM - Genome Biol Evol (2015)

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.

View Article: PubMed Central - PubMed

Affiliation: Univ. Bordeaux, ISVV, EA 4577 Œnologie, Villenave d'Ornon, France Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.

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Phylogenetic and phylogenomic reconstructions of O. oeni by four different methods. Phylogenetic reconstruction by MLST was compared against phylogenomic reconstructions by Tetra, SNP, and ANIm. When possible, bootstrap values were calculated by doing 1,000 iterations (values indicated in bottom legend). Major genetic groups are indicated as in the legend. Strains coming from the same product (champagne, cider) are indicated when they form a single cluster.
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evv084-F2: Phylogenetic and phylogenomic reconstructions of O. oeni by four different methods. Phylogenetic reconstruction by MLST was compared against phylogenomic reconstructions by Tetra, SNP, and ANIm. When possible, bootstrap values were calculated by doing 1,000 iterations (values indicated in bottom legend). Major genetic groups are indicated as in the legend. Strains coming from the same product (champagne, cider) are indicated when they form a single cluster.

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.


Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines.

Campbell-Sills H, El Khoury M, Favier M, Romano A, Biasioli F, Spano G, Sherman DJ, Bouchez O, Coton E, Coton M, Okada S, Tanaka N, Dols-Lafargue M, Lucas PM - Genome Biol Evol (2015)

Phylogenetic and phylogenomic reconstructions of O. oeni by four different methods. Phylogenetic reconstruction by MLST was compared against phylogenomic reconstructions by Tetra, SNP, and ANIm. When possible, bootstrap values were calculated by doing 1,000 iterations (values indicated in bottom legend). Major genetic groups are indicated as in the legend. Strains coming from the same product (champagne, cider) are indicated when they form a single cluster.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494047&req=5

evv084-F2: Phylogenetic and phylogenomic reconstructions of O. oeni by four different methods. Phylogenetic reconstruction by MLST was compared against phylogenomic reconstructions by Tetra, SNP, and ANIm. When possible, bootstrap values were calculated by doing 1,000 iterations (values indicated in bottom legend). Major genetic groups are indicated as in the legend. Strains coming from the same product (champagne, cider) are indicated when they form a single cluster.
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.

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.

View Article: PubMed Central - PubMed

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
Related in: MedlinePlus