BIOGEOGRAPHY AND GENETIC DIVERSITY OF <Italic>CUCUMBER</italic> <Italic>MOSAIC</italic> <Italic>CUCUMOVIRUS</italic> (CMV) AND THE ROLE OF SATELLITE RNA IN SYMPTOM DEVELOPMENT
Snap bean (Phaseolusvulgaris L.) and pepper (Capsicumannuum L.) crops in the Midwest and Northeast United States have been affected by a complex of plant virus epidemics since 2000. Cucumbermosaiccucumovirus (CMV) was consistently recovered from infected plants. The reasons behind these outbreaks are not well known. Here, the phylogeographic structure and genetic variation of CMV isolates was investigated at the local, state and national levels. The genetic diversity was low, with the 2b gene possessing the greatest variability. CMV subgroup I was identified as the predominant subgroup in the US and in Wisconsin. Furthermore, both subgroups IA and IB were recognized among CMV isolates. In Wisconsin, subgroup IA was the only subgroup obtained from snap bean, whereas the CMV population in pepper consisted of both subgroups. However, no association between phylogenetic groups, location or year was observed in the US and Wisconsin. CMV subpopulations from different fields within Wisconsin were not genetically differentiated in most instances, while there were differences between the two hosts in this investigation. Evidence for genetic exchange was rare in natural populations of CMV. Purifying selection was determined as the major natural force, whereas positively selected sites were detected in the 2a, 2b and CP proteins. In addition, novel satellite RNAs (satRNA) were discovered in CMV field isolates of snap bean for the first time. Results obtained from a greenhouse bioassay illustrated that this extra RNA exacerbated symptom development and hastened the time of symptom expression in snap bean. In contrast, satRNAs attenuated symptoms in tobacco. In conclusion, our analyses provided a snap shot of the genetic diversity and phylogenetic relationships among representative CMV isolates in the US and Wisconsin. It seems that the recent virus epidemics may not have been due to the invasion of a new CMV subgroup in snap bean and probably a founder effect has played a role in shaping the CMV structure in this host. The presence of satRNA in the CMV population together with the introduction of a novel vector, the soybean aphid (Aphisglycines Matsumura), may be partial explanations for the emergence of these virus outbreaks.