Genetic diversity of Strawberry mottle virus genome

The strawberry mottle virus (SMoV), which seriously reduces the productivity of strawberries, is a huge threat to the strawberry production. A systematic study of the distribution, structural variation and genetic diversity of SMoV in Shanxi will lay a certain theoretical foundation for the prevention and control of strawberry virus diseases. In this study, 159 strawberry leaves were randomly collected from 7 major strawberry growing areas in Shanxi Province for RT-PCR detection. The cp genes of positive samples were sequenced and analyzed through MEGA5, SDTv 1.2, DnaSP v5.10 and RDP v.4.31. RT-PCR detection showed that 65 samples of the 159 strawberry leaves were positive with a detection rate of 38.46%. The 65 positive samples were isolated, sequenced, and cloned to obtain 3 SMoV isolates, the phylogenetic tree analysis of which combined with 22 online SMoV isolates showed the 25 SMoV isolates were divided into three groups with group 1 containing 14 isolates from China , group 2 containing 10 isolates from Canada, Japan, and the United States and group 3 containing 1 isolate from Japan. The results of selective pressure analysis and neutrality test in group 1 and group 2 showed there were significant genetic differences between group 1 and group 2, the neutrality test was negative, and the SMoV population was expanded. Sequence similarity analysis displayed that the nucleotide identity range and the consistency range of amino acids was 94.68%~99.53% and 98.12%~99.84% respectively, which showed high similarity. This study demonstrated that SMoV has high genetic variation, and the negative selection pressure may be the cause of SMoV genetic diversity, which provides theoretical guidance for SMoV in Shanxi.