title: Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151.
abstract: Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease.
authors.affiliation: Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia.
authors.forename: Mario L
authors.initials: ML
authors.lastname: Arrieta-Ortiz
authors.forename: Luis M
authors.initials: LM
authors.lastname: Rodríguez-R
authors.forename: Álvaro  L
authors.initials: Á
authors.lastname: Pérez-Quintero
authors.forename: Lucie
authors.initials: L
authors.lastname: Poulin
authors.forename: Ana C
authors.initials: AC
authors.lastname: Díaz
authors.forename: Nathalia
authors.initials: N
authors.lastname: Arias Rojas
authors.forename: Cesar
authors.initials: C
authors.lastname: Trujillo
authors.forename: Mariana
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authors.lastname: Restrepo Benavides
authors.forename: Rebecca
authors.initials: R
authors.lastname: Bart
authors.forename: Jens
authors.initials: J
authors.lastname: Boch
authors.forename: Tristan
authors.initials: T
authors.lastname: Boureau
authors.forename: Armelle
authors.initials: A
authors.lastname: Darrasse
authors.forename: Perrine
authors.initials: P
authors.lastname: David
authors.forename: Thomas
authors.initials: T
authors.lastname: Dugé de Bernonville
authors.forename: Paula
authors.initials: P
authors.lastname: Fontanilla
authors.forename: Lionel
authors.initials: L
authors.lastname: Gagnevin
authors.forename: Fabien
authors.initials: F
authors.lastname: Guérin
authors.forename: Marie-Agnès
authors.initials: MA
authors.lastname: Jacques
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Lauber
authors.forename: Pierre
authors.initials: P
authors.lastname: Lefeuvre
authors.forename: Cesar
authors.initials: C
authors.lastname: Medina
authors.forename: Edgar
authors.initials: E
authors.lastname: Medina
authors.forename: Nathaly
authors.initials: N
authors.lastname: Montenegro
authors.forename: Alejandra
authors.initials: A
authors.lastname: Muñoz Bodnar
authors.forename: Laurent D
authors.initials: LD
authors.lastname: Noël
authors.forename: Juan F
authors.initials: JF
authors.lastname: Ortiz Quiñones
authors.forename: Daniela
authors.initials: D
authors.lastname: Osorio
authors.forename: Carolina
authors.initials: C
authors.lastname: Pardo
authors.forename: Prabhu B
authors.initials: PB
authors.lastname: Patil
authors.forename: Stéphane
authors.initials: S
authors.lastname: Poussier
authors.forename: Olivier
authors.initials: O
authors.lastname: Pruvost
authors.forename: Isabelle
authors.initials: I
authors.lastname: Robène-Soustrade
authors.forename: Robert P
authors.initials: RP
authors.lastname: Ryan
authors.forename: Javier
authors.initials: J
authors.lastname: Tabima
authors.forename: Oscar G
authors.initials: OG
authors.lastname: Urrego Morales
authors.forename: Christian
authors.initials: C
authors.lastname: Vernière
authors.forename: Sébastien
authors.initials: S
authors.lastname: Carrere
authors.forename: Valérie
authors.initials: V
authors.lastname: Verdier
authors.forename: Boris
authors.initials: B
authors.lastname: Szurek
authors.forename: Silvia
authors.initials: S
authors.lastname: Restrepo
authors.forename: Camilo
authors.initials: C
authors.lastname: López
authors.forename: Ralf
authors.initials: R
authors.lastname: Koebnik
authors.forename: Adriana
authors.initials: A
authors.lastname: Bernal
mesh_terms: D016680:Genome, Bacterial / Q000235:genetics; D018598:Minisatellite Repeats / Q000235:genetics; D014774:Virulence / Q000235:genetics; D053532:Xanthomonas axonopodis / Q000235:genetics* / Q000472:pathogenicity