title: Development of a variable number of tandem repeats typing scheme for the bacterial rice pathogen Xanthomonas oryzae pv. oryzicola.
abstract: Xanthomonas oryzae pv. oryzicola is an important bacterial pathogen responsible for outbreaks of bacterial leaf streak (BLS) on rice, mostly occurring in Asia and parts of Africa. To better monitor epidemics and assess population structures, efficient tools that allow the precise identification and diagnosis of pathogenic populations are needed. In this study, we explored variable numbers of tandem repeats (VNTR) as a fast, reliable, and cost-effective molecular typing tool. Screening of three X. oryzae pv. oryzicola genome sequences (Philippine strain BLS256, Chinese strain GX01, and Malian strain MAI10) predicted 28 candidate VNTR loci. Primer pairs for polymerase chain reaction (PCR) amplification of all 28 loci were designed and applied to a panel of 20 X. oryzae pv. oryzicola strains originating from Asia and Africa. Sequencing of PCR amplicons revealed 25 robust and polymorphic VNTR loci that are shared among Asian and African X. oryzae pv. oryzicola strains. A dendrogram constructed from 25 VNTR loci indicated that most Asian strains are clearly discriminated from African strains. However, in agreement with previous reports, one strain from Mali is related to Asian strains, pointing to a possible introduction of Asian strains to the African continent. The new VNTR-based tool described here is useful for studies of population structures and epidemiological monitoring of X. oryzae pv. oryzicola.
authors.affiliation: Institut de Recherche pour le Developpement, Montpellier, France.
authors.forename: Shuai
authors.initials: S
authors.lastname: Zhao
authors.forename: Lucie
authors.initials: L
authors.lastname: Poulin
authors.forename: Luis M
authors.initials: LM
authors.lastname: Rodriguez-R
authors.forename: Natalia Forero
authors.initials: NF
authors.lastname: Serna
authors.forename: Shu-Yan
authors.initials: SY
authors.lastname: Liu
authors.forename: Issa
authors.initials: I
authors.lastname: Wonni
authors.forename: Boris
authors.initials: B
authors.lastname: Szurek
authors.forename: Valérie
authors.initials: V
authors.lastname: Verdier
authors.forename: Jan E
authors.initials: JE
authors.lastname: Leach
authors.forename: Yong-Qiang
authors.initials: YQ
authors.lastname: He
authors.forename: Jia-Xun
authors.initials: JX
authors.lastname: Feng
authors.forename: Ralf
authors.initials: R
authors.lastname: Koebnik
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D018598:Minisatellite Repeats; D012275:Oryza / Q000382:microbiology*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D014974:Xanthomonas / Q000235:genetics* / Q000472:pathogenicity
chemical_list: D017931:DNA Primers