Department of Agriculture and Fisheries, Ecosciences Precinct, Brisbane, QLD, Australia.
Agriculture Victoria Research Division, Department of Economic Development, Jobs, Transport & Resources, AgriBio, La Trobe University, Bundoora, Victoria, 3083, Australia.
BMC Genomics. 2019 Apr 23;20(1):310. doi: 10.1186/s12864-019-5600-x.
The genetic diversity in Australian populations of Xanthomonas species associated with bacterial leaf spot in tomato, capsicum and chilli were compared to worldwide bacterial populations. The aim of this study was to confirm the identities of these Australian Xanthomonas species and classify them in comparison to overseas isolates. Analysis of whole genome sequence allows for the investigation of bacterial population structure, pathogenicity and gene exchange, resulting in better management strategies and biosecurity.
Phylogenetic analysis of the core genome alignments and SNP data grouped strains in distinct clades. Patterns observed in average nucleotide identity, pan genome structure, effector and carbohydrate active enzyme profiles reflected the whole genome phylogeny and highlight taxonomic issues in X. perforans and X. euvesicatoria. Circular sequences with similarity to previously characterised plasmids were identified, and plasmids of similar sizes were isolated. Potential false positive and false negative plasmid assemblies were discussed. Effector patterns that may influence virulence on host plant species were analysed in pathogenic and non-pathogenic xanthomonads.
The phylogeny presented here confirmed X. vesicatoria, X. arboricola, X. euvesicatoria and X. perforans and a clade of an uncharacterised Xanthomonas species shown to be genetically distinct from all other strains of this study. The taxonomic status of X. perforans and X. euvesicatoria as one species is discussed in relation to whole genome phylogeny and phenotypic traits. The patterns evident in enzyme and plasmid profiles indicate worldwide exchange of genetic material with the potential to introduce new virulence elements into local bacterial populations.
对与番茄、辣椒和辣椒细菌性叶斑病相关的澳大利亚黄单胞菌种群的遗传多样性与世界范围内的细菌种群进行了比较。本研究的目的是确认这些澳大利亚黄单胞菌的身份，并将其与海外分离株进行分类。全基因组序列分析可用于研究细菌种群结构、致病性和基因交换，从而制定更好的管理策略和生物安全措施。
核心基因组比对和 SNP 数据分析的系统发育分析将菌株分为不同的分支。平均核苷酸同一性、泛基因组结构、效应子和碳水化合物活性酶谱观察到的模式反映了全基因组系统发育，突出了穿孔黄单胞菌和 euvesicatoria 黄单胞菌的分类问题。鉴定了与先前描述的质粒具有相似性的圆形序列，并分离出大小相似的质粒。讨论了潜在的假阳性和假阴性质粒组装。分析了致病性和非致病性黄单胞菌中可能影响宿主植物物种致病力的效应子模式。
本文提出的系统发育证实了 vesicatoria、arboricola、euvesicatoria 和 perforans 黄单胞菌，以及一个未鉴定的黄单胞菌属物种的分支，该分支在遗传上与本研究的所有其他菌株明显不同。穿孔黄单胞菌和 euvesicatoria 作为一个物种的分类地位与全基因组系统发育和表型特征有关。酶和质粒谱中的模式表明，遗传物质在全球范围内交换，有可能将新的毒力元件引入当地细菌种群。
