PLoS ONE (Jan 2013)

Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme.

  • Yanjun Li,
  • Yujun Cui,
  • Baizhong Cui,
  • Yanfeng Yan,
  • Xianwei Yang,
  • Haidong Wang,
  • Zhizhen Qi,
  • Qingwen Zhang,
  • Xiao Xiao,
  • Zhaobiao Guo,
  • Cong Ma,
  • Jing Wang,
  • Yajun Song,
  • Ruifu Yang

DOI
https://doi.org/10.1371/journal.pone.0066567
Journal volume & issue
Vol. 8, no. 6
p. e66567

Abstract

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Variable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a "14+12" loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized "14+12" loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis.