Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW 2568, Australia.
Phytopathology. 2024 Jul;114(7):1480-1489. doi: 10.1094/PHYTO-12-23-0490-R. Epub 2024 Jul 11.
is a plant-pathogenic bacterium associated with a diverse range of host plant species. It has undergone substantial reclassification and currently consists of 14 different subspecies or pathovars that are responsible for a wide range of plant diseases. Whole-genome sequencing (WGS) provides a cutting-edge advantage over other diagnostic techniques in epidemiological and evolutionary studies of . because it has a higher discriminatory power and is replicable across laboratories. WGS also allows for the improvement of multilocus sequence typing (MLST) schemes. In this study, we used genome sequences of isolates from the NCBI RefSeq database to develop a seven-gene MLST scheme that yielded 19 sequence types (STs) that correlated with phylogenetic clades of . subspecies or pathovars. Using this MLST scheme, we examined 2,911 species assemblies from NCBI GenBank and identified 15 novel STs from 37 isolates that were misclassified in NCBI. In total, we identified 545 assemblies from GenBank with 95% average nucleotide identity to the type strain, and all were classified as one of the 34 STs. All MLST classifications correlated with a phylogenetic position inferred from alignments using 92 conserved genes. We observed several instances where strains from different pathovars formed closely related monophyletic clades and shared the same ST, indicating that further investigation of the validity of these pathovars is required. Our MLST scheme described here is a robust tool for rapid classification of pathovars using WGS and a powerful method for further comprehensive taxonomic revision of . pathovars.
是一种与多种宿主植物物种相关的植物病原细菌。它经历了大量的重新分类，目前由 14 个不同的亚种或致病型组成，这些亚种或致病型负责广泛的植物疾病。全基因组测序 (WGS) 在 的流行病学和进化研究中提供了比其他诊断技术更具优势，因为它具有更高的辨别力，并且可以在实验室之间复制。WGS 还允许改进多位点序列分型 (MLST) 方案。在这项研究中，我们使用来自 NCBI RefSeq 数据库的 分离株的基因组序列，开发了一个七基因 MLST 方案，该方案产生了 19 个与 亚种或致病型的系统发育枝相关的序列型 (ST)。使用该 MLST 方案，我们检查了来自 NCBI GenBank 的 2911 个物种组装，并从 37 个在 NCBI 中被错误分类的分离株中鉴定出 15 个新的 ST。总共，我们从 GenBank 中鉴定出了 545 个组装，这些组装与 模式株的 95%平均核苷酸同一性，并且全部被归类为 34 个 ST 之一。所有 MLST 分类都与使用 92 个保守基因进行比对推断的系统发育位置相关。我们观察到一些来自不同致病型的菌株形成密切相关的单系枝并共享相同的 ST 的情况，这表明需要进一步调查这些致病型的有效性。我们在这里描述的 MLST 方案是使用 WGS 对 致病型进行快速分类的强大工具，也是进一步全面修订 致病型分类的有力方法。
