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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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Cluster analysis on the ortholog groups of O. oeni. Ortholog groups are represented in the form of heatmap, where each cell displays the number of CDS contained in the group for each strain. The number of CDS of for each ortholog ranges from 0 to 8.
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evv084-F5: Cluster analysis on the ortholog groups of O. oeni. Ortholog groups are represented in the form of heatmap, where each cell displays the number of CDS contained in the group for each strain. The number of CDS of for each ortholog ranges from 0 to 8.

Mentions: A search for specific genes and SNP was also performed in order to determine if some of them could explain some characteristics of the group where they are present. To determine whether the groups A and B differ by the absence or presence of specific genes, we performed a cluster analysis that depicts the distribution of the 2,469 ortholog groups of the O. oeni pangenome among the 50 strains (fig. 5). The resulting heat map reveals two major clusters for genetic groups A and B, with strain IOEB_C52 being the most external of cluster B. It is also possible to observe a clade made of strains that come from champagne. The genes specific of groups of strains were identified by calculating Shannon Entropy (H) for each ortholog group. A total of 94 orthologs specific to strains either of group A, B, champagne or strain IOEB_C52 were detected (table 4A). They encode hypothetical proteins, transcription regulators and proteins involved in diverse functions, but none that is obviously related to ethanol resistance (supplementary table S1, Supplementary Material online). Genes that are present exclusively in groups A or B are limited to hypothetical proteins. Genes unique to IOEB_C52 include, besides the Trs system mentioned before, a phosphoglycolate phosphatase, lanthionine biosynthesis proteins, transporters, sugar utilisation, and nucleotide metabolism proteins. At the same time, this strain lacks a set of five hypothetical proteins that are present in all the other strains. The four strains isolated from champagne share a unique set of nine genes, seven coding for hypothetical proteins, one for a primase–helicase, and one for cellulose 1,4-beta-cellobiosidase. They also lack, along with the strain IOEB_S450, a gene encoding an esterase C. The loss of this gene in two of the champagne strains had already been reported (Mohedano et al. 2014). A detailed list of all the discriminating orthologs among strains of group A, B, C, champagne and cider is shown in supplementary table S1, Supplementary Material online.Fig. 5.—


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)

Cluster analysis on the ortholog groups of O. oeni. Ortholog groups are represented in the form of heatmap, where each cell displays the number of CDS contained in the group for each strain. The number of CDS of for each ortholog ranges from 0 to 8.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv084-F5: Cluster analysis on the ortholog groups of O. oeni. Ortholog groups are represented in the form of heatmap, where each cell displays the number of CDS contained in the group for each strain. The number of CDS of for each ortholog ranges from 0 to 8.
Mentions: A search for specific genes and SNP was also performed in order to determine if some of them could explain some characteristics of the group where they are present. To determine whether the groups A and B differ by the absence or presence of specific genes, we performed a cluster analysis that depicts the distribution of the 2,469 ortholog groups of the O. oeni pangenome among the 50 strains (fig. 5). The resulting heat map reveals two major clusters for genetic groups A and B, with strain IOEB_C52 being the most external of cluster B. It is also possible to observe a clade made of strains that come from champagne. The genes specific of groups of strains were identified by calculating Shannon Entropy (H) for each ortholog group. A total of 94 orthologs specific to strains either of group A, B, champagne or strain IOEB_C52 were detected (table 4A). They encode hypothetical proteins, transcription regulators and proteins involved in diverse functions, but none that is obviously related to ethanol resistance (supplementary table S1, Supplementary Material online). Genes that are present exclusively in groups A or B are limited to hypothetical proteins. Genes unique to IOEB_C52 include, besides the Trs system mentioned before, a phosphoglycolate phosphatase, lanthionine biosynthesis proteins, transporters, sugar utilisation, and nucleotide metabolism proteins. At the same time, this strain lacks a set of five hypothetical proteins that are present in all the other strains. The four strains isolated from champagne share a unique set of nine genes, seven coding for hypothetical proteins, one for a primase–helicase, and one for cellulose 1,4-beta-cellobiosidase. They also lack, along with the strain IOEB_S450, a gene encoding an esterase C. The loss of this gene in two of the champagne strains had already been reported (Mohedano et al. 2014). A detailed list of all the discriminating orthologs among strains of group A, B, C, champagne and cider is shown in supplementary table S1, Supplementary Material online.Fig. 5.—

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