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首页> 外文期刊>Applied Microbiology >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
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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

机译：水稻黄单胞菌致病性白叶枯病和细菌叶片条纹监测和局部流行病学的新型多基因座可变数目串联重复分析工具

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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.
机译：多基因座可变数目串联重复分析（MLVA）对于常规分型和调查天然微生物种群的遗传结构非常有效。在热带和温带水稻种植国家中，米氏黄单胞菌的两种截然不同的病害可导致作物的重大损失。细菌的叶条纹是由米曲霉X病毒引起的。 Oryzicola和细菌性叶枯病是由X. oryzae pv引起的。水稻对于后者，文献中描述了两个遗传谱系。我们开发了一种通用的MLVA分型工具，用于识别三个米曲霉的遗传谱系和进行流行病学分析。根据三个米曲霉谱系的10个草图或完整基因组序列中它们的存在和多态性，并通过对每个谱系20个菌株中感兴趣的基因座子集进行VNTR测序，选择了16个候选可变数串联重复（VNTR）基因座。然后将MLVA-16方案应用于代表不同病原体和地理位置的338株米曲霉菌株。 MLVA基因座之间的连锁不平衡是通过不同尺度下的指数关联来计算的，而这16个基因座与56个米曲霉菌株的MLSA数据显示出线性的Mantel相关性，表明它们提供了良好的系统发生信号。此外，对不同谱系菌株的分析表明，有可能使用该方案在较小的空间尺度上进行更深入的流行病学调查。

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