Core genome MLST for epidemiological and evolutionary analyses of phytopathogenic Xanthomonas citri
Core genome MLST for epidemiological and evolutionary analyses of phytopathogenic Xanthomonas citri
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用于植物病原柑橘黄单胞菌流行病学和进化分析的核心基因组 MLST
DOI：
10.1101/2022.12.20.521341
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Ragupathy R
中科院分区：
文献类型：
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作者：
Ragupathy R
柑橘黄单胞菌是柑橘细菌性溃烂病的病原菌，在南美、美国、中国和日本等地的柑橘生产中造成了包括甜橙、柠檬和西柚在内的柑橘产业的重大经济损失。其他X。Citrisubsp.致病变种对大豆、菜豆、芒果、石榴和腰果等作物的病害负有责任。追踪X的传播。多年来，人们使用了几种不同的分型方法来进行柑橘疾病的研究，但最近使用基因组测序的研究对于理解物种内的进化关系，包括XCC病型之间的根本差异是关键。在本研究中，我们开发了X的核心基因组多位点分型方案(CgMLST)。基于250个基因组组成的多个X的例子。柑橘亚种A、A*和Aw、X.Citrisubsp.MalacearumandX.柑橘病原菌、多聚糖、甘氨酸、棕榈酸酯、芒果、葡萄孢霉、葡萄孢霉和X。柑橘病原菌包括巴赫氏菌和粉锈菌。该数据集包括100个新的XCC分离株的基因组测序。CgMLST计划基于250个基因组中的1618个核心基因，已在PubMLST(https://pubmlst.org/organisms/xanthomonas-citri/).实施根据cgMLST数据生成的葡萄树最小跨度系统发育图和iTOL邻接系统发育图分别用4分钟、15分钟和36小时将几乎相同的分离物分组解析为基于SNP的核心基因组邻接系统发育图。这些基因解决了XCC致病类型和x的相同分组。Citrisubsp.和致病变种。柑橘黄绿僵菌应被证明是研究这一关键植物病原菌的一个越来越有价值的资源。用户可以在PubMLST.org上提交基因组和相关元数据，以便与以前描述的分离株进行比较，以便快速确定这些病原体的地方、国家和全球流行病学特征，并检查进化关系。
Xanthomonas citrisubspeciescitri(XCC) is the cause of bacterial citrus canker, responsible for major economic losses to the citrus industry that includes sweet orange, lime and grapefruit production in regions including South America, United States, China and Japan. OtherX. citrisubsp. and pathovars are responsible for diseases in crops such as soy bean, common bean, mango, pomegranate and cashew. Tracing the spread ofX. citridisease has been performed using several different typing methods over the years but recent studies using genomic sequencing have been key to understanding evolutionary relationships within the species including fundamental differences between XCC pathotypes.In this study we developed a core genome multilocus typing scheme (cgMLST) forX. citribased upon 250 genomes comprising multiple examples ofX. citrisubsp.citripathotypes A, A* and Aw,X. citrisubsp.malvacearumandX. citripathovarsaurantifolii, fuscans, glycines, malvacearum, mangiferaeindicae, viticola, vignicolaand single isolates ofX. citripathovarsdieffenbachiaeandpunicae. This dataset included genomic sequencing of 100 novel XCC isolates. The cgMLST scheme, based upon 1618 core genes across 250 genomes, has been implemented at PubMLST (https://pubmlst.org/organisms/xanthomonas-citri/). Grapetree minimum-spanning, and iTOL Neighbour-joining phylogenies generated from cgMLST data resolved almost identical groupings of isolates to a core genome SNP - based neighbour joining phylogeny taking 4 min, 15 min and 36 h respectively. These resolved identical groupings of XCC pathotypes andX. citrisubsp. and pathovars.X. citricgMLST should prove to be an increasingly valuable resource for the study of this key species of plant pathogenic bacteria. Users can submit genomic and associated metadata to compare with previously characterised isolates at PubMLST.org to allow rapid characterization of local, national and global epidemiology of these pathogens and examine evolutionary relationships.
开放式细菌种群基因组学：BIGSDB软件，pubmlst.org网站及其应用。
影响因子：
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作者：
Jolley KA;Bray JE;Maiden MCJ
通讯作者：
Maiden MCJ
DOI：
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发表时间：
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期刊：
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影响因子：
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作者：
Systems Biology
通讯作者：
Systems Biology