State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing 100193, China.
Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
Viruses. 2022 Nov 9;14(11):2481. doi: 10.3390/v14112481.
Southern tomato amalgavirus (STV) is a cryptic pathogen that is abundant in tomato production fields and intensifies the resurgence of tomato yellow stunt disease (ToYSD), together with other phytoviruses. Here, we mapped the geographical and genomic diversity, phylogenetics, and evolutionary dynamics of STV. We found that STV prevailed across China and Pakistan, with a maximum average rate of infection of 43.19% in Beijing, China, and 40.08% in Punjab, Pakistan. Subsequently, we amplified, cloned, and annotated the complete genome sequences of STV isolates from L. in China (OP548653 and OP548652) and Pakistan (MT066231) using Sanger and next-generation sequencing (NGS). These STV isolates displayed close evolutionary relationships with others from Asia, America, and Europe. Whole-genome-based molecular diversity analysis showed that STV populations had 33 haplotypes with a gene diversity (Hd) of 0.977 and a nucleotide diversity (π) of 0.00404. The genetic variability of RNA-dependent RNA-polymerase (RdRp) was higher than that of the putative coat protein (CP) p42. Further analysis revealed that STV isolates were likely to be recombinant but with a lower-to-moderate level of confidence. With a variable distribution pattern of positively and negatively selected sites, negative selection pressure predominantly acted on p42 and RdRp. These findings elaborated on the molecular variability and evolutionary trends among STV populations across major tomato-producing regions of the world.
南方番茄曲叶病毒（STV）是一种隐匿性病原体，在番茄生产田中大量存在，并与其他植物病毒一起加剧了番茄黄化曲叶病（ToYSD）的死灰复燃。在这里，我们对 STV 的地理和基因组多样性、系统发育和进化动态进行了绘图。我们发现 STV 在中国和巴基斯坦普遍存在，在中国北京的感染率最高，平均为 43.19%，在巴基斯坦旁遮普省为 40.08%。随后，我们使用 Sanger 和下一代测序（NGS）对来自中国（OP548653 和 OP548652）和巴基斯坦（MT066231）的 STV 分离株进行了全基因组扩增、克隆和注释。这些 STV 分离株与来自亚洲、美洲和欧洲的其他分离株具有密切的进化关系。基于全基因组的分子多样性分析表明，STV 群体有 33 种单倍型，基因多样性（Hd）为 0.977，核苷酸多样性（π）为 0.00404。RNA 依赖性 RNA 聚合酶（RdRp）的遗传变异性高于假定的外壳蛋白（CP）p42。进一步分析表明，STV 分离株可能是重组的，但置信度较低至中等。正选择和负选择位点的分布模式具有变异性，负选择压力主要作用于 p42 和 RdRp。这些发现详细阐述了世界主要番茄生产地区 STV 群体的分子变异性和进化趋势。
