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. 2015 Jan;81(2):688-98.
doi: 10.1128/AEM.02768-14. Epub 2014 Nov 14.

New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae

L Poulin  1 , P Grygiel  2 , M Magne  2 , L Gagnevin  2 , L M Rodriguez-R  1 , N Forero Serna  1 , S Zhao  1 , M El Rafii  1 , S Dao  3 , C Tekete  3 , I Wonni  4 , O Koita  3 , O Pruvost  2 , V Verdier  1 , C Vernière  2 , R Koebnik  5
Affiliations

New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae

L Poulin et al. Appl Environ Microbiol. 2015 Jan.

Abstract

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.

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Figures

FIG 1
FIG 1
Venn diagram of VNTR loci that were included in the general typing scheme for X. oryzae. The positions of loci in the diagram correspond to their predicted polymorphism within each lineage. The four gray squares represent the four quadruplex-PCR pools.
FIG 2
FIG 2
Minimum spanning tree of African X. oryzae pv. oryzae strains using BioNumerics 7.1 and detailed view of the Malian clonal complex of strains from Niono and Sélingue (inset). The differences in repeat numbers per locus between two haplotypes is given between the circles. The circle sizes are proportional to the number of strains per haplotype. The red lines correspond to single-locus variants, green lines correspond to double-locus variants, black lines correspond to triple-locus variants, dashed lines correspond to quadruple-locus variants, and light-gray lines correspond to more than quadruple-locus variants.
FIG 3
FIG 3
Minimum spanning tree of X. oryzae pv. oryzicola strains using BioNumerics 7.1. For details, see the legend to Fig. 2.
FIG 4
FIG 4
Minimum spanning tree of Asian X. oryzae pv. oryzae strains using BioNumerics 7.1 and detailed view of a Philippine clonal complex of strains from Calauan and Mabitac (inset). The differences in repeat numbers per locus between two haplotypes are given between the circles. For details, see the legend to Fig. 2.
See this image and copyright information in PMC

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