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            <funder>This work was supported by the French Agence Nationale de la Recherche (ANR-10-BLAN-1723) and the French Direction Generale de l'Armement (DGA) (2010 34 0006). Lucie Poulin is grateful to DGA for her Ph.D. fellowship (2011 60 091). Shuai Zhao is grateful to the Bourses Doctorales en Alternance from the French Embassy in China, the program of postgraduate education and research of Guangxi (T31036), and the plans for joint training of doctoral students and academic visiting of postgraduates of Guangxi University (L300278) for support.</funder>
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              <p>Multilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryzicola, and bacterial leaf blight is caused by X. oryzae pv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the three X. oryzae genetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the three X. oryzae lineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains of X. oryzae representing different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56 X. oryzae strains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales.</p>
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