Department of Biological Sciences, Universidad de los Andes, Bogotá D.C., Colombia.
CIRAD, UMR PHIM, Montpellier, France.
PLoS One. 2023 May 11;18(5):e0285491. doi: 10.1371/journal.pone.0285491. eCollection 2023.
Cassava Bacterial Blight (CBB) is a destructive disease widely distributed in the different areas where this crop is grown. Populations studies have been performed at local and national scales revealing a geographical genetic structure with temporal variations. A global epidemiology analysis of its causal agent Xanthomonas phaseoli pv. manihotis (Xpm) is needed to better understand the expansion of the disease for improving the monitoring of CBB. We targeted new tandem repeat (TR) loci with large repeat units, i.e. minisatellites, that we multiplexed in a scheme of Multi-Locus Variable number of TR Analysis (MLVA-8). This genotyping scheme separated 31 multilocus haplotypes in three clusters of single-locus variants and a singleton within a worldwide collection of 93 Xpm strains isolated over a period of fifty years. The major MLVA-8 cluster 1 grouped strains originating from all countries, except the unique Chinese strain. On the contrary, all the Xpm strains genotyped using the previously developed MLVA-14 microsatellite scheme were separated as unique haplotypes. We further propose an MLVA-12 scheme which takes advantage of combining TR loci with different mutation rates: the eight minisatellites and four faster evolving microsatellite markers, for global epidemiological surveillance. This MLVA-12 scheme identified 78 haplotypes and separated most of the strains in groups of double-locus variants (DLV) supporting some phylogenetic relationships. DLV groups were subdivided into closely related clusters of strains most often sharing the same geographical origin and isolated over a short period, supporting epidemiological relationships. The main MLVA-12 DLV group#1 was composed by strains from South America and all the African strains. The MLVA-12 scheme combining both minisatellite and microsatellite loci with different discriminatory power is expected to increase the accuracy of the phylogenetic signal and to minimize the homoplasy effects. Further investigation of the global epidemiology of Xpm will be helpful for a better control of CBB worldwide.
木薯细菌性条斑病（CBB）是一种破坏性疾病，广泛分布于种植该作物的不同地区。在地方和国家范围内进行了种群研究，揭示了具有时间变化的地理遗传结构。需要对其致病因子黄单胞菌木薯致病变种（Xpm）进行全球流行病学分析，以更好地了解疾病的扩展，从而改善 CBB 的监测。我们以具有大重复单元的新串联重复（TR）基因为目标，即微卫星，我们将其多路复用在多位点可变重复数分析（MLVA-8）的方案中。该基因分型方案将在全球范围内收集的 93 株 Xpm 菌株在 50 年的时间内分离出的 31 个多位点单倍型分为三个单基因座变体的单倍型簇和一个单倍型。主要的 MLVA-8 簇 1 聚集了来自所有国家的菌株，除了独特的中国菌株。相反，使用先前开发的 MLVA-14 微卫星方案对所有 Xpm 菌株进行的基因分型均分离为独特的单倍型。我们进一步提出了 MLVA-12 方案，该方案利用结合具有不同突变率的 TR 基因座：八个微卫星和四个快速进化的微卫星标记，用于全球流行病学监测。该 MLVA-12 方案确定了 78 个单倍型，并将大多数菌株分为双基因座变体（DLV）组，支持某些系统发育关系。DLV 组被进一步细分为密切相关的菌株簇，这些菌株簇通常具有相同的地理起源和在短时间内分离出来，支持流行病学关系。主要的 MLVA-12 DLV 组#1 由来自南美洲和所有非洲菌株的菌株组成。该 MLVA-12 方案结合了具有不同鉴别力的微卫星和微卫星基因座，预计将提高系统发育信号的准确性，并最小化同形性效应。进一步研究 Xpm 的全球流行病学将有助于更好地控制全球的 CBB。
