title: Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome.
abstract: BACKGROUND
  The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot (pv. campestris), bacterial blight of stock (pv. incanae) or bacterial leaf spot (pv. raphani).
  
  
  RESULTS
  In this study, we extended the genomic coverage of the species by sequencing and annotating the genomes of strains from pathovar incanae (CFBP 1606R and CFBP 2527R), pathovar raphani (CFBP 5828R) and a pathovar formerly named barbareae (CFBP 5825R). While comparative analyses identified a large core ORFeome at the species level, the core type III effectome was limited to only three putative type III effectors (XopP, XopF1 and XopAL1). In Xanthomonas, these effector proteins are injected inside the plant cells by the type III secretion system and contribute collectively to virulence. A deep and strand-specific RNA sequencing strategy was adopted in order to experimentally refine genome annotation for strain CFBP 5828R. This approach also allowed the experimental definition of novel ORFs and non-coding RNA transcripts. Using a constitutively active allele of hrpG, a master regulator of the type III secretion system, a HrpG-dependent regulon of 141 genes co-regulated with the type III secretion system was identified. Importantly, all these genes but seven are positively regulated by HrpG and 56 of those encode components of the Hrp type III secretion system and putative effector proteins.
  
  
  CONCLUSIONS
  This dataset is an important resource to mine for novel type III effector proteins as well as for bacterial genes which could contribute to pathogenicity of X. campestris.
authors.affiliation: INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.
authors.forename: Brice
authors.initials: B
authors.lastname: Roux
authors.affiliation: INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Bolot
authors.affiliation: INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|Present address: INRA, UMR Institut de Génétique, Environnement et Protection des Plantes, F-35653, Le Rheu, France.
authors.forename: Endrick
authors.initials: E
authors.lastname: Guy
authors.affiliation: INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|Present address: INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49070, Beaucouzé, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Denancé
authors.affiliation: INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|Université de Toulouse, Université Paul Sabatier, F-31062, Toulouse, France.
authors.forename: Martine
authors.initials: M
authors.lastname: Lautier
authors.affiliation: INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|INPT-Université de TOULOUSE, ENSAT, Avenue de l'Agrobiopole, Auzeville-Tolosane, 31326, Castanet-Tolosan, France.
authors.forename: Marie-Françoise
authors.initials: MF
authors.lastname: Jardinaud
authors.affiliation: INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49070, Beaucouzé, France.
authors.forename: Marion
authors.initials: M
authors.lastname: Fischer-Le Saux
authors.affiliation: INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49070, Beaucouzé, France.
authors.forename: Perrine
authors.initials: P
authors.lastname: Portier
authors.affiliation: INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49070, Beaucouzé, France.
authors.forename: Marie-Agnès
authors.initials: MA
authors.lastname: Jacques
authors.affiliation: CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410, Saint-Pierre, La Réunion, France.
authors.forename: Lionel
authors.initials: L
authors.lastname: Gagnevin
authors.affiliation: CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410, Saint-Pierre, La Réunion, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Pruvost
authors.affiliation: INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Lauber
authors.affiliation: INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|Université de Toulouse, Université Paul Sabatier, F-31062, Toulouse, France.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Arlat
authors.affiliation: INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.|CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Carrère
authors.affiliation: Institut de Recherche pour le Développement (IRD), UMR IRD-CIRAD-UM2 Interactions Plantes-Microorganismes-Environnement (IPME), F-34394, Montpellier, Cedex 5, France.
authors.forename: Ralf
authors.initials: R
authors.lastname: Koebnik
authors.affiliation: INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France. laurent.noel@toulouse.inra.fr.|CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326, Castanet-Tolosan, France. laurent.noel@toulouse.inra.fr.
authors.forename: Laurent D
authors.initials: LD
authors.lastname: Noël
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D023281:Genomics; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D018085:Regulon / Q000235:genetics; D016959:Xanthomonas campestris / Q000235:genetics* / Q000276:immunology
chemical_list: D001426:Bacterial Proteins