Xanthomonas campestris pv. musacearum NCPPB4433 Genome Sequencing. Xanthomonas vasicola pv. musacearum NCPPB 4433

Although classified as a member of the species Xanthomonas campestris, we recently showed that Xcm is more properly considered to be derived from the species Xanthomonas vasicola. We previously generated complete genome sequences for a single isolate of Xcm from banana in Uganda and for a single isolate of X. vasicola pathovar vasculorum (Xvv) that is non-pathogenic on banana and was isolated from sugarcane in South Africa. These two isolates share identical gyrase B DNA sequences. Differences between these two genome sequences revealed several candidate genes that might play a role in adaptation to the banana host. These may also be useful tools in identifying genes for deployment of disease resistance. Specifically, these included homologues of effectors secreted and translocated by the type III secretion system (T3SS). T3SS effectors have previously been shown to contribute to host-specificity acting as virulence and/or avirulence factors [refs]. Previous work showed that Xcm is a highly monomorphic pathogen and no specific genetic differences have yet been detected among different isolates using traditional typing and diagnostic methods . Affordable complete genome sequencing now makes it feasible to discover previously hidden genetic diversity among isolates of a monomorphic pathogen, though this approach has rarely been applied to phytopathogens as yet. Here we use genome-wide sequence data to discover a set of single-nucleotide polymorphisms (SNPs) among East African isolates of Xcm. These SNPs have potential as molecular markers for phylogeographic studies of the epidemiology and spread of the pathogen. Our analysis suggests the presence of at least two major sub-lineages of the pathogen; Xcm isolates from Uganda, Kenya, Tanzania and Burundi are genetically distinct from isolates collected in Ethiopia, DR Congo and Rwanda, suggesting that the current outbreaks of BXW on Musa species in the region have more than one origin.

尽管被归类为野油菜黄单胞菌（Xanthomonas campestris）的成员，但我们近期的研究表明，Xcm更合理的分类归属应为起源于维管束黄单胞菌（Xanthomonas vasicola）的类群。我们此前已完成对乌干达一株香蕉来源的Xcm分离株，以及一株来自南非甘蔗、对香蕉无致病性的维管束黄单胞菌维管束致病型（X. vasicola pathovar vasculorum, Xvv）分离株的全基因组测序。这两株分离株的促旋酶B（gyrase B）DNA序列完全一致。比对两份全基因组序列后，我们发现了数个可能参与香蕉宿主适应性的候选基因。此类基因亦可作为工具，用于鉴定可应用于抗病性部署的相关基因。具体而言，这些候选基因包含III型分泌系统（type III secretion system, T3SS）所分泌并转运的效应蛋白同源物。既往研究已证实，III型分泌系统效应蛋白可作为致病力和/或无毒因子，参与宿主特异性互作[参考文献]。此前的研究表明，Xcm是一种高度单态性的病原菌，采用传统分型与诊断方法尚未在不同分离株间检测到明确的遗传差异。如今，经济实惠的全基因组测序技术已使得发掘单态性病原菌分离株中此前未被发现的遗传多样性成为可能，尽管该方法目前仍极少应用于植物病原菌。本研究利用全基因组序列数据，在东非Xcm分离株中鉴定得到一组单核苷酸多态性（single-nucleotide polymorphisms, SNPs）标记。此类单核苷酸多态性可作为分子标记，用于该病原菌流行病学与传播规律的系统地理学研究。分析结果显示，该病原菌至少存在两个主要的亚谱系：来自乌干达、肯尼亚、坦桑尼亚以及布隆迪的Xcm分离株，与埃塞俄比亚、刚果民主共和国以及卢旺达采集的分离株在遗传层面存在显著分化；这表明该区域当前在芭蕉属（Musa）植物上暴发的BXW疫情，存在至少两个以上的起源。