Core-Genome Multilocus Sequence Typing for Epidemiological and Evolutionary Analyses of Phytopathogenic Xanthomonas citri.
Core-Genome Multilocus Sequence Typing for Epidemiological and Evolutionary Analyses of Phytopathogenic Xanthomonas citri.
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DOI：
10.1128/aem.02101-22
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发表时间：
2023-05-31
影响因子：
4.4
通讯作者：
Enright, M. C.
中科院分区：
文献类型：
--
作者：
Ragupathy, R.;Jolley, K. A.;Zamuner, C.;Jones, J. B.;Redfern, J.;Behlau, F.;Ferreira, H.;Enright, M. C.
柑橘黄单胞菌柑橘溃疡病是柑橘细菌性溃疡病的主要病原，给柑橘产业带来了巨大的经济损失。X.柑橘属亚种和致病变种是大豆、菜豆、芒果、石榴和腰果中的病害的原因。X.柑橘疾病已经使用几种分型方法进行了跟踪，但最近使用基因组测序的研究是了解物种内进化关系的关键，包括X之间的根本差异。柑桔属柑橘属致病型在这里，我们描述了一个核心基因组多位点序列分型（cgMLST）计划X。citri基于250个基因组，包括X.柑桔属柑桔致病型A、A* 和Aw; X.柑桔属malvacearum; X. Citri pv.橙叶变种富斯坎峰甘氨酸光伏芒果树致病变种viticola和pv. vignicola和X. Citri pv.花叶万年青和花叶病毒石榴。该数据集包括100个新X的基因组测序。柑桔属柑桔属分离物。cgMLST基于250个基因组中的1，618个核心基因，在PubMLST（https：//pubmlst.org/organisms/xanthomonas-citri/）中实施。从cgMLST数据生成的GrapeTree最小生成树和交互式生命树（iTOL）相邻连接同源性将几乎相同的分离株分组解析为基于核心基因组单核苷酸多态性（SNP）的相邻连接同源性。这些解决了X的相同分组。柑桔属citri致病型和X.柑桔属亚种和致病变种。X.柑橘cgMLST应该被证明是一个越来越有价值的资源，用于研究这种关键物种的植物病原细菌。用户可以提交基因组数据和相关的元数据，以便与PubMLST上先前表征的分离株进行比较，从而快速表征这些病原体的地方、国家和全球流行病学，并检查进化关系。柑橘黄单胞菌（Xanthomonascitri）是一种对柑橘产业，特别是甜橙橙子生产造成重大经济损失的植物病原体。几个亚种和病原体是公认的，宿主范围包括大豆，菜豆，芒果，石榴和腰果等。最近的基因组研究表明，适应宿主的X。citri亚种和致病变种以及X.柑桔属柑橘属致病型形成不同的分支。在这项研究中，我们描述了一个核心基因组多位点序列分型（cgMLST）计划，这个物种，可以快速，稳健地区分这些生态不同的，主机适应的分支。我们已经在PubMLST上建立了这个方案和包含基因组序列和元数据的相关数据库，用户可以用自己的基因组序列进行查询以确定X。柑桔亚种、致病变型和致病型。X. citri cgMLST应该被证明是一个非常宝贵的工具，流行病学和这种主要的植物病原体的进化研究。
Xanthomonas citri subsp. citri is the cause of bacterial citrus canker, responsible for major economic losses to the citrus industry. X. citri subspecies and pathovars are responsible for diseases in soybean, common bean, mango, pomegranate, and cashew. X. citri disease has been tracked using several typing methods, but recent studies using genomic sequencing have been key to understanding the evolutionary relationships within the species, including fundamental differences among X. citri subsp. citri pathotypes. Here, we describe a core-genome multilocus sequence typing (cgMLST) scheme for X. citri based on 250 genomes comprising multiple examples of X. citri subsp. citri pathotypes A, A*, and Aw; X. citri subsp. malvacearum; X. citri pv. aurantifolii, pv. fuscans, pv. glycines, pv. mangiferaeindicae, pv. viticola, and pv. vignicola; and single isolates of X. citri pv. dieffenbachiae and pv. punicae. This data set included genomic sequencing of 100 novel X. citri subsp. citri isolates. cgMLST, based on 1,618 core genes across 250 genomes, is implemented at PubMLST (https://pubmlst.org/organisms/xanthomonas-citri/). GrapeTree minimum-spanning tree and Interactive Tree of Life (iTOL) neighbor-joining phylogenies generated from the cgMLST data resolved almost identical groupings of isolates to a core-genome single nucleotide polymorphism (SNP)-based neighbor-joining phylogeny. These resolved identical groupings of X. citri subsp. citri pathotypes and X. citri subspecies and pathovars. X. citri cgMLST should prove to be an increasingly valuable resource for the study of this key species of plant-pathogenic bacteria. Users can submit genomic data and associated metadata for comparison with previously characterized isolates at PubMLST to allow the rapid characterization of the local, national, and global epidemiology of these pathogens and examine evolutionary relationships. IMPORTANCE Xanthomonas citri is a plant pathogen that causes major economic losses to the citrus industry and sweet orange production in particular. Several subspecies and pathogens are recognized, with host ranges including soybean, common bean, mango, pomegranate, and cashew, among others. Recent genomic studies have shown that host-adapted X. citri subspecies and pathovars and X. citri subsp. citri pathotypes form distinct clades. In this study, we describe a core-genome multilocus sequence typing (cgMLST) scheme for this species that can rapidly and robustly discriminate among these ecologically distinct, host-adapted clades. We have established this scheme and associated databases containing genomic sequences and metadata at PubMLST, which users can interrogate with their own genome sequences to determine X. citri subspecies, pathovars, and pathotypes. X. citri cgMLST should prove to be an invaluable tool for the study of the epidemiology and evolution of this major plant pathogen.
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