Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity
Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity
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DOI：
10.1128/aem.02993-16
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发表时间：
2017-05-01
影响因子：
4.4
通讯作者：
Patil, Prabhu B.
中科院分区：
文献类型：
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作者：
Bansal, Kanika;Midha, Samriti;Patil, Prabhu B.
柑桔溃疡病是由柑桔黄单胞菌致病变种Xanthomonascitripv.柑桔的一种严重病害。早期利用管家基因的系统发育研究表明，X。Citri PV.柑橘黄单胞菌与许多其它致病型相关，这些致病型可统称为柑橘黄单胞菌致病型（XCP）。从目前的研究中，我们报告了18个XCP的基因组序列，并将其与公共领域中的4个XCP进行了比较。在一个基于XCP基因组标记基因的树中，所有XCP形成一个单系簇，表明它们来自一个共同的祖先。使用模式菌株的系统基因组分析进一步确定所有XCP属于一个物种。核心基因组的克隆分析揭示了两个主要的谱系内的单系群组成的一些克隆变体的存在。顺便说一句，这些XCP中的大多数首先在印度被发现，证实了它们的克隆关系和共同起源。比较分析揭示了一个开放的泛基因组和这些XCP的菌株间基因组通量的作用，因为他们从一个共同的祖先多样化。尽管III型基因效应子存在广泛的变异，但我们确定了三个核心效应子，它们在抗性育种计划中可能是有价值的。总的来说，生态亲缘的基因组检查使我们能够剖析X的巨大基因组潜力。重要性宿主专化是高度进化的病原体如黄单胞菌属植物病原细菌的特征之一。由于宿主涉及主要作物和经济上重要的水果，如柑橘，详细了解感染不同植物的此类菌株的多样性和演变对于检疫目的很重要。在本研究中，我们进行了基因组成员的遗传学和生态学定义的黄单胞菌菌株致病性不同的植物，包括柑橘。该组包括最古老的黄单胞菌致病变种，也包括最近出现的致病变种，在一个特定的国家，他们是地方病。我们的高通量基因组研究为由严重病原体及其生态亲属组成的独特谱系的进化提供了新的见解，表明了快速和近期多样化的性质，范围和模式。此外，从物种的水平，克隆变体，该研究揭示了有趣的基因组模式的多样化的黄单胞菌谱系，也许会激发仔细研究的宿主范围内的致病变种。
Citrus canker, caused by Xanthomonas citri pv. citri, is a serious disease of citrus plants worldwide. Earlier phylogenetic studies using housekeeping genes revealed that X. citri pv. citri is related to many other pathovars, which can be collectively referred as Xanthomonas citri pathovars (XCPs). From the present study, we report the genome sequences of 18 XCPs and compared them with four XCPs available in the public domain. In a tree based on phylogenomic marker genes, all the XCPs form a monophyletic cluster, suggesting their origin from a common ancestor. Phylogenomic analysis using the type strain further established that all the XCPs belong to one species. Clonal analysis of the core genome revealed the presence of two major lineages within this monophyletic cluster consisting of some clonal variants. Incidentally, the majority of these XCPs were first noticed in India, corroborating their clonal relationship and their common origin. Comparative analysis revealed an open pan-genome and the role of interstrain genomic flux of these XCPs since their diversification from a common ancestor. Even though there are wide variations in type III gene effectomes, we identified three core effectors which can be valuable in resistance-breeding programs. Overall, genomic examination of ecological relatives allowed us to dissect the tremendous genomic potential of X. citri species to rapidly evolve into specialized strains infecting diverse crop plants.IMPORTANCE Host specialization is one of the characteristic features of highly evolved pathogens such as the Xanthomonas group of phytopathogenic bacteria. Since the hosts involve staple crops and economically important fruits such as citrus, detailed understanding of the diversity and evolution of such strains infecting diverse plants is important for quarantine purposes. In the present study, we carried out genomic investigation of members of a phylogenetically and ecologically defined group of Xanthomonas strains pathogenic to diverse plants, including citrus. This group includes the oldest Xanthomonas pathovars and also recently emerged pathovars in a particular country where they are endemic. Our high-throughput genomic study has provided novel insights into the evolution of a unique lineage consisting of serious pathogens and their ecological relatives, suggesting the nature, scope, and pattern of rapid and recent diversification. Further, from the level of species to that of clonal variants, the study revealed interesting genomic patterns in diversification of a Xanthomonas lineage and perhaps will inspire careful study of the host range of the included pathovars.