Department of Plant Pathology, University of Florida, Gainesville, Florida, USA.
Department of Plant Pathology, China Agricultural University, Beijing, China.
Appl Environ Microbiol. 2024 Oct 23;90(10):e0131324. doi: 10.1128/aem.01313-24. Epub 2024 Sep 18.
Bacterial leaf spot of pepper (BSP), primarily caused by ), poses a significant challenge to pepper production worldwide. Despite its impact, the genetic diversity of this pathogen remains underexplored, which limits our understanding of its population structure. To bridge this knowledge gap, we conducted a comprehensive analysis using 103 strains isolated from pepper in southwest Florida to characterize genomic and type III effector (T3E) variation in this population. Phylogenetic analysis of core genomes revealed a major distinct genetic lineage associated with amylolytic activity. This amylolytic lineage was represented in strains globally. Molecular clock analysis dated the emergence of amylolytic strains in to around 1972. Notably, non-amylolytic strains possessed a single base pair frameshift deletion in the ⍺-amylase gene yet retained a conserved C-terminus. GUS assay revealed the expression of two open reading frames in non-amylolytic strains, one at the N-terminus and another that starts 136 base pairs upstream of the ⍺-amylase gene. Analysis of T3Es in the Florida population identified variation in 12 effectors, including two classes of mutations in that prevent AvrBs2 from triggering a hypersensitive response in -resistant pepper plants. Knowledge of T3E variation could be used for effector-targeted disease management. This study revealed previously undescribed population structure in this economically important pathogen.IMPORTANCEBacterial leaf spot (BSP), a significant threat to pepper production globally, is primarily caused by (). Limited genomic data has hindered detailed studies on its population diversity. This study analyzed the whole-genome sequences of 103 strains from peppers in southwest Florida, along with additional global strains, to explore the pathogen's diversity. The study revealed two major distinct genetic groups based on their amylolytic activity, the ability to break down starch, with non-amylolytic strains having a mutation in the ⍺-amylase gene. Additionally, two classes of mutations in the gene were found, leading to susceptibility in pepper plants with the resistance gene, a commercially available resistance gene for BSP. These findings highlight the need to forecast the emergence of such strains, identify genetic factors for innovative disease management, and understand how this pathogen evolves and spreads.
辣椒细菌性叶斑病（BSP）主要由 引起，对全球辣椒生产构成重大挑战。尽管其影响很大，但该病原体的遗传多样性仍未得到充分探索，这限制了我们对其种群结构的理解。为了弥补这一知识空白，我们对佛罗里达州西南部的 103 株从辣椒中分离出的菌株进行了全面分析，以描述该种群的基因组和 III 型效应物（T3E）变异。核心基因组的系统发育分析显示，与淀粉水解活性相关的一个主要的独特遗传谱系。在全球范围内，该淀粉水解谱系代表了 株菌株。分子钟分析表明，淀粉水解菌株出现在 年左右。值得注意的是，非淀粉水解菌株在 ⍺-淀粉酶基因中存在单个碱基对移码缺失，但保留了保守的 C 末端。GUS 测定表明，非淀粉水解菌株在 ⍺-淀粉酶基因上游 136 个碱基对处起始的一个开放阅读框和 N 末端表达两个开放阅读框。对佛罗里达州 种群中的 T3E 分析鉴定了 12 种效应物的变异，包括 中阻止 AvrBs2 在 -抗性辣椒植物中引发过敏反应的两类突变。对 T3E 变异的了解可用于针对效应物的疾病管理。本研究揭示了该具有经济重要性的病原体以前未描述的种群结构。
重要性：细菌性叶斑病（BSP）是一种对全球辣椒生产构成重大威胁的疾病，主要由 （）引起。有限的基因组数据阻碍了对其种群多样性的详细研究。本研究分析了来自佛罗里达州西南部辣椒的 103 株 菌株的全基因组序列，以及来自其他地区的全球菌株，以探讨该病原体的多样性。研究结果表明，根据其淀粉水解活性，存在两个主要的不同遗传群体，即能够分解淀粉的能力，而非淀粉水解菌株的 ⍺-淀粉酶基因发生突变。此外，还发现 基因中有两类突变，导致具有 抗性基因的辣椒植株易感， 抗性基因是一种用于 BSP 的商业上可用的抗性基因。这些发现强调了需要预测此类菌株的出现，确定用于创新疾病管理的遗传因素，并了解该病原体如何进化和传播。
