Redila Carla Dizon, Phipps Savannah, Nouri Shahideh
Department of Plant Pathology, College of Agriculture, Kansas State University, Manhattan, KS, United States.
Front Microbiol. 2021 Jul 30;12:699078. doi: 10.3389/fmicb.2021.699078. eCollection 2021.
Wheat streak mosaic (WSM), a viral disease affecting cereals and grasses, causes substantial losses in crop yields. Wheat streak mosaic virus (WSMV) is the main causal agent of the complex, but mixed infections with Triticum mosaic virus (TriMV) and High plains wheat mosaic emaravirus (HPWMoV) were reported as well. Although resistant varieties are effective for the disease control, a WSMV resistance-breaking isolate and several potential resistance-breaking isolates have been reported, suggesting that viral populations are genetically diverse. Previous phylogenetic studies of WSMV were conducted by focusing only on the virus coat protein (CP) sequence, while there is no such study for either TriMV or HPWMoV. Here, we studied the genetic variation and evolutionary mechanisms of natural populations of WSM-associated viruses mainly in Kansas fields and fields in some other parts of the Great Plains using high-throughput RNA sequencing. In total, 28 historic and field samples were used for total RNA sequencing to obtain full genome sequences of WSM-associated viruses. Field survey results showed WSMV as the predominant virus followed by mixed infections of WSMV + TriMV. Phylogenetic analyses of the full genome sequences demonstrated that WSMV Kansas isolates are widely distributed in sub-clades. In contrast, phylogenetic analyses for TriMV isolates showed no significant diversity. Recombination was identified as the major evolutionary force of WSMV and TriMV variation in KS fields, and positive selection was detected in some encoding genomic regions in the genome of both viruses. Furthermore, the full genome sequence of a second Kansas HPWMoV isolate was reported. Here, we also identified previously unknown WSMV isolates in the Great Plains sharing clades and high nucleotide sequence similarities with Central Europe isolates. The findings of this study will provide more insights into the genetic structure of WSM-associated viruses and, in turn, help in improving strategies for disease management.
小麦线条花叶病（WSM）是一种影响谷类作物和禾本科植物的病毒性疾病，会导致作物产量大幅损失。小麦线条花叶病毒（WSMV）是该病害复合体的主要致病因子，但也有报道称存在与小麦花叶病毒（TriMV）和高平原小麦花叶内病毒（HPWMoV）的混合感染情况。尽管抗性品种对病害防治有效，但已有报道称出现了一个打破WSMV抗性的分离株以及几个潜在的打破抗性的分离株，这表明病毒群体在基因上具有多样性。此前对WSMV的系统发育研究仅聚焦于病毒外壳蛋白（CP）序列，而对于TriMV或HPWMoV则没有此类研究。在此，我们利用高通量RNA测序技术，主要针对堪萨斯州以及大平原其他一些地区的田间，研究了与WSM相关病毒自然群体的遗传变异和进化机制。总共使用了28个历史样本和田间样本进行总RNA测序，以获取与WSM相关病毒的全基因组序列。田间调查结果显示，WSMV是主要病毒，其次是WSMV + TriMV的混合感染。对全基因组序列的系统发育分析表明，堪萨斯州的WSMV分离株广泛分布于各个亚分支中。相比之下，对TriMV分离株的系统发育分析显示没有显著的多样性。重组被确定为堪萨斯州田间WSMV和TriMV变异的主要进化驱动力，并且在这两种病毒基因组的一些编码区域检测到了正选择。此外，还报道了堪萨斯州第二个HPWMoV分离株的全基因组序列。在此，我们还在大平原地区鉴定出了此前未知的WSMV分离株，它们与中欧分离株共享分支且核苷酸序列相似度很高。本研究的结果将为与WSM相关病毒的遗传结构提供更多见解，进而有助于改进病害管理策略。
