title: A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage.
abstract: MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epidemics on a global scale. Xanthomonas citri pv. citri is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of Xanthomonas citri pv. citri strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these in silico data, an optimized MLVA scheme was developed to assess the global diversity of this monomorphic bacterium. Thirty-one minisatellite loci (MLVA-31) were selected to assess the genetic structure of 129 strains representative of the worldwide pathological and genetic diversity of X. citri pv. citri. Based on Discriminant Analysis of Principal Components (DAPC), four pathotype-specific clusters were defined. DAPC cluster 1 comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31. MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the Xanthomonas citri genotyping database (http://www.biopred.net/MLVA/).
authors.affiliation: UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Pruvost
authors.affiliation: UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France.
authors.forename: Maxime
authors.initials: M
authors.lastname: Magne
authors.affiliation: UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France.
authors.forename: Karine
authors.initials: K
authors.lastname: Boyer
authors.affiliation: UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France.
authors.forename: Alice
authors.initials: A
authors.lastname: Leduc
authors.affiliation: Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs (RPB), IRD-CIRAD-UM2, Montpellier, France; Institut de Génétique et Microbiologie, UMR 8621, Université de Paris-Sud, Orsay, France; Institut de Génétique et Microbiologie, UMR 8621, CNRS, Orsay, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Tourterel
authors.affiliation: Institut de Génétique et Microbiologie, UMR 8621, Université de Paris-Sud, Orsay, France; Institut de Génétique et Microbiologie, UMR 8621, CNRS, Orsay, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Drevet
authors.affiliation: UMR Biologie et Génétiques des Interactions Plante-Parasite (BGPI), CIRAD, Montpellier, France.
authors.forename: Virginie
authors.initials: V
authors.lastname: Ravigné
authors.affiliation: UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France.
authors.forename: Lionel
authors.initials: L
authors.lastname: Gagnevin
authors.affiliation: UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Université de la Réunion, Saint Pierre, La Réunion, France.
authors.forename: Fabien
authors.initials: F
authors.lastname: Guérin
authors.affiliation: UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Chiroleu
authors.affiliation: Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs (RPB), IRD-CIRAD-UM2, Montpellier, France.
authors.forename: Ralf
authors.initials: R
authors.lastname: Koebnik
authors.affiliation: Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs (RPB), IRD-CIRAD-UM2, Montpellier, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Verdier
authors.affiliation: UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Vernière
mesh_terms: D015373:Bacterial Typing Techniques; D002957:Citrus / Q000382:microbiology*; D005798:Genes, Bacterial; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D010935:Plant Diseases / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences; D014974:Xanthomonas / Q000235:genetics*