Genetic Structure and Molecular Variability of Cucumber mosaic virus Isolates in the United States

Cucumber mosaic virus (CMV) has a worldwide distribution and the widest host range of any known plant virus. From 2000 to 2012, epidemics of CMV severely affected the production of snap bean (Phaseulos vulgaris L.) in the Midwest and Northeastern United States. Virus diversity leading to emergence of new strains is often considered a significant factor in virus epidemics. In addition to epidemics, new disease phenotypes arising from genetic exchanges or mutation can compromise effectiveness of plant disease management strategies. Here, we captured a snapshot of genetic variation of 32 CMV isolates collected from different regions of the U.S including new field as well as historic isolates. Nucleotide diversity (π) was low for U.S. CMV isolates. Sequence and phylogenetic analyses revealed that CMV subgroup I is predominant in the US and further showed that the CMV population is a mixture of subgroups IA and IB. Furthermore, phylogenetic analysis suggests likely reassortment between subgroups IA and IB within five CMV isolates. Based on phylogenetic and computational analysis, recombination between subgroups I and II as well as IA and IB in RNA 3 was detected. This is the first report of recombination between CMV subgroups I and II. Neutrality tests illustrated that negative selection was the major force operating upon the CMV genome, although some positively selected sites were detected for all encoded proteins. Together, these data suggest that different regions of the CMV genome are under different evolutionary constraints. These results also delineate composition of the CMV population in the US, and further suggest that recombination and reassortment among strain subgroups does occur but at a low frequency, and point towards CMV genomic regions that differ in types of selection pressure.黄瓜花叶病毒（Cucumber mosaic virus, CMV）是一种全球分布、寄主范围为已知植物病毒中最广泛的种类。2000年至2012年间，CMV流行严重影响了美国中西部与东北部地区菜豆（Phaseolus vulgaris L.）的生产。病毒多样性引发新毒株出现，常被认为是病毒流行的关键影响因素之一。除流行事件外，由基因重组或突变产生的新型病害表型，还可能削弱植物病害防控策略的实施效果。本研究对采集自美国不同区域的32株CMV分离物进行了遗传变异快照式采样，其中既包含新分离的田间毒株，也涵盖历史分离物。美国CMV分离物的核苷酸多样性（π）水平较低。序列与系统发育分析结果显示，CMV亚组I是美国境内的优势亚组，进一步表明CMV种群为亚组IA与IB的混合群体。此外，系统发育分析提示，其中5株CMV分离物可能存在IA与IB亚组间的基因重配现象。基于系统发育与计算分析，本研究在RNA3片段中检测到了亚组I与II以及IA与IB亚组间的重组事件。这是首次关于CMV亚组I与II间发生重组的报道。中性检验结果表明，负选择是作用于CMV基因组的主要进化压力，尽管所有编码蛋白均检测到少量正选择位点。综合来看，本研究数据表明CMV基因组的不同区域承受着不同的进化约束。本研究结果明确了美国境内CMV种群的组成结构，进一步证实毒株亚组间确实存在重组与基因重配现象，但发生频率较低，同时指出了承受不同选择压力类型的CMV基因组区域。