@article{fdi:010063668,
  title = {{N}ew multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by {X}anthomonas oryzae},
  author = {{P}oulin, {L}ucie and {G}rygiel, {P}. and {M}agne, {M}. and {G}agnevin, {L}. and {R}odriguez, {L}. {M}. and {S}erna, {N}. {F}. and {Z}hao, {S}. and {E}l {R}afii, {M}. and {D}ao, {S}. and {T}ekete, {C}. and {W}onni, {I}. and {K}oita, {O}. and {P}ruvost, {O}. and {V}erdier, {V}al{\'e}rie and {V}erni{\`e}re, {C}. and {K}oebnik, {R}alf},
  editor = {},
  language = {{ENG}},
  abstract = {{M}ultilocus variable-number tandem-repeat analysis ({MLVA}) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. {T}wo distinct pathovars of {X}anthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. {B}acterial leaf streak is caused by {X}. oryzae pv. oryzicola, and bacterial leaf blight is caused by {X}. oryzae pv. oryzae. {F}or the latter, two genetic lineages have been described in the literature. {W}e developed a universal {MLVA} typing tool both for the identification of the three {X}. oryzae genetic lineages and for epidemiological analyses. {S}ixteen 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. {T}he {MLVA}-16 scheme was then applied to 338 strains of {X}. oryzae representing different pathovars and geographical locations. {L}inkage disequilibrium between {MLVA} loci was calculated by index association on different scales, and the 16 loci showed linear {M}antel correlation with {MLSA} data on 56 {X}. oryzae strains, suggesting that they provide a good phylogenetic signal. {F}urthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales.},
  keywords = {{AFRIQUE} ; {ASIE}},
  booktitle = {},
  journal = {{A}pplied and {E}nvironmental {M}icrobiology},
  volume = {81},
  numero = {2},
  pages = {688--698},
  ISSN = {0099-2240},
  year = {2015},
  DOI = {10.1128/aem.02768-14},
  URL = {https://www.documentation.ird.fr/hor/fdi:010063668},
}