Abstract:

To analyze the molecular variation and genetic diversity of strawberry mottle virus (SMoV), high-throughput sequencing (HTS), RT-PCR combined with 3ʹ and 5ʹ RACE were used to obtain the complete genome sequence of SMoV Fujian isolate. The results showed that RNA1 and RNA2 of SMoV consisted of 7034 nt and 6354 nt, and both contained one large ORF, encoding polyprotein P1 and P2, respectively. The homology of SMoV Fujian isolate and other fifteen SMoV isolates was analyzed. The nucleotide and amino acid homology of RNA1 was 79.2%-96.8% and 89.0%-99.5%, respectively. The nucleotide and amino acid homology of RNA2 was 77.9%-97.8% and 89.9%-98.9%, respectively. Among the encoding proteins of SMoV Fujian isolate, only the viral genome-linked protein was the most conserved, the nucleotide and amino acid sequences of other proteins were variable compared to other 15 SMoV isolates. The Fujian isolate and some other Chinese isolates are in a big branch, and most closely related to Chinese isolate DGHY3. The genomic structure of Fujian isolate is consistent with other SMoV isolates. Nucleotide sequence and amino acid sequence of Fujian isolate have obvious molecular variation. Fujian isolate and the other Chinese isolates have abundant diversity, and there is geographical relativity in evolution.

Key words: strawberry mottle virus, high-throughput sequencing, complete genome sequence, molecular variation, phylogenetic tree analysis