Pruvost Olivier, Magne Maxime, Boyer Karine, Leduc Alice, Tourterel Christophe, Drevet Christine, Ravigné Virginie, Gagnevin Lionel, Guérin Fabien, Chiroleu Frédéric, Koebnik Ralf, Verdier Valérie, Vernière Christian
UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France.
Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs (RPB), IRD-CIRAD-UM2, Montpellier, France; Institut de Génétique et Microbiologie, UMR 8621, Université de Paris-Sud, Orsay, France; Institut de Génétique et Microbiologie, UMR 8621, CNRS, Orsay, France.
PLoS One. 2014 Jun 4;9(6):e98129. doi: 10.1371/journal.pone.0098129. eCollection 2014.
MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epidemics on a global scale. Xanthomonas citri pv. citri is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of Xanthomonas citri pv. citri strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these in silico data, an optimized MLVA scheme was developed to assess the global diversity of this monomorphic bacterium. Thirty-one minisatellite loci (MLVA-31) were selected to assess the genetic structure of 129 strains representative of the worldwide pathological and genetic diversity of X. citri pv. citri. Based on Discriminant Analysis of Principal Components (DAPC), four pathotype-specific clusters were defined. DAPC cluster 1 comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31. MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the Xanthomonas citri genotyping database (http://www.biopred.net/MLVA/).
多位点可变数目串联重复序列分析（MLVA）已被广泛用于研究单态性人类病原菌的流行病学和进化问题，但尚未用于具有农业重要性的细菌性植物病原菌，尽管此类工具将有助于我们更好地理解其流行病学以及全球范围内的疫情历史。柑橘黄龙病菌是多个国家的检疫性生物，也是全球柑橘产业的主要威胁。我们筛选了柑橘黄龙病菌菌株IAPAR 306以及系统发育相关的黄单胞菌的基因组中的串联重复序列。基于这些计算机模拟数据，开发了一种优化的MLVA方案，以评估这种单态细菌的全球多样性。选择了31个微卫星位点（MLVA-31）来评估代表柑橘黄龙病菌全球病理和遗传多样性的129个菌株的遗传结构。基于主成分判别分析（DAPC），定义了四个致病型特异性聚类。DAPC聚类1包含与20世纪柑橘黄龙病菌主要地理扩张有关的菌株。12个位点的一个子集（MLVA-12）解析了总多样性的89%，并与MLVA-31揭示的遗传结构相匹配。建议将MLVA-12用于柑橘黄龙病菌的常规流行病学鉴定，而MLVA-31用于系统发育和群体遗传学研究。MLVA-31为国际柑橘黄龙病菌基因分型和数据共享提供了一个契机。本研究中生成的MLVA-31数据已存入柑橘黄龙病菌基因分型数据库（http://www.biopred.net/MLVA/）。
