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

hal.structure.identifierUnité de Recherche Oenologie [Villenave d'Ornon] [OENO]
hal.structure.identifierFondazione Edmund Mach - Functional genomics
dc.contributor.authorCAMPBELL-SILLS, Hugo
hal.structure.identifierUnité de Recherche Oenologie [Villenave d'Ornon] [OENO]
dc.contributor.authorEL KHOURY, Mariette
hal.structure.identifierLaffort [Floirac]
dc.contributor.authorFAVIER, Marion
hal.structure.identifierFondazione Edmund Mach - Functional genomics
dc.contributor.authorROMANO, Andrea
hal.structure.identifierFondazione Edmund Mach - Functional genomics
dc.contributor.authorBIASIOLI, Franco
hal.structure.identifierDipartimento di Scienze Agrarie, degli Alimenti e dell'Ambiente - Department of the Sciences of Agriculture, Food and Environment [University of Foggia]
dc.contributor.authorSPANO, Giuseppe
hal.structure.identifierfrom patterns to models in computational biodiversity and biotechnology [PLEIADE]
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
dc.contributor.authorSHERMAN, David James
hal.structure.identifierGénome et Transcriptome - Plateforme Génomique [GeT-PlaGe]
hal.structure.identifierLaboratoire de Génétique Cellulaire [LGC]
dc.contributor.authorBOUCHEZ, Olivier
hal.structure.identifierLaboratoire Universitaire de Biodiversité et Ecologie Microbienne [LUBEM]
dc.contributor.authorCOTON, Emmanuel
hal.structure.identifierLaboratoire Universitaire de Biodiversité et Ecologie Microbienne [LUBEM]
dc.contributor.authorCOTON, Monika
hal.structure.identifierTokyo University of Agriculture and Technology [TUAT]
dc.contributor.authorOKADA, Sanae
hal.structure.identifierTokyo University of Agriculture and Technology [TUAT]
dc.contributor.authorTANAKA, Naoto
hal.structure.identifierUnité de Recherche Oenologie [Villenave d'Ornon] [OENO]
hal.structure.identifierInstitut Polytechnique de Bordeaux [Bordeaux INP]
dc.contributor.authorDOLS-LAFARGUE, Marguerite
hal.structure.identifierUnité de Recherche Oenologie [Villenave d'Ornon] [OENO]
dc.contributor.authorLUCAS, Patrick M
dc.date.issued2015-05-31
dc.identifier.issn1759-6653
dc.description.abstractEnOenococcus oeni is a lactic acid bacteria species encountered particularly in wine, where it achieves the malolactic fermentation. Molecular typing methods have previously revealed that the species is made of several genetic groups of strains, some being specific to certain types of wines, ciders or regions. Here, we describe 36 recently released O. oeni genomes and the phylogenomic analysis of these 36 plus 14 previously reported genomes. We also report three genome sequences of the sister species Oenococcus kitaharae that were used for phylogenomic reconstructions. Phylogenomic and population structure analyses performed revealed that the 50 O. oeni genomes delineate two major groups of 12 and 37 strains, respectively, named A and B, plus a putative group C, consisting of a single strain. 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 strain from putative group C was isolated from cider and genetically closer to group B strains. 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.
dc.language.isoen
dc.publisherSociety for Molecular Biology and Evolution
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subjectOenococcus oeni
dc.subjectdomestication
dc.subjectgenomics
dc.subjectpopulation structure
dc.subject.enphylogeny
dc.title.enPhylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines.
dc.typeArticle de revue
dc.identifier.doi10.1093/gbe/evv084
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
dc.subject.halSciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire/Génomique, Transcriptomique et Protéomique [q-bio.GN]
dc.description.sponsorshipEuropeMulti-strain indigenous Yeast and Bacterial starters for ‘Wild-ferment’ Wine production
bordeaux.journalGenome Biology and Evolution
bordeaux.page1506-18
bordeaux.volume7
bordeaux.issue6
bordeaux.peerReviewedoui
hal.identifierhal-01202801
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01202801v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Genome%20Biology%20and%20Evolution&rft.date=2015-05-31&rft.volume=7&rft.issue=6&rft.spage=1506-18&rft.epage=1506-18&rft.eissn=1759-6653&rft.issn=1759-6653&rft.au=CAMPBELL-SILLS,%20Hugo&EL%20KHOURY,%20Mariette&FAVIER,%20Marion&ROMANO,%20Andrea&BIASIOLI,%20Franco&rft.genre=article


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