RNA Secondary Structure and Sequence Variability of the 3' End of Strawberry Mild Yellow Edge Virus Genome

The specific segment in 3' terminal region of strawberry mild yellow edge virus (SMYEV) genome was amplified by 3' rapid amplification of cDNA ends (RACE). Ten Chinese isolates were sequenced. Sequence analysis of coat protein gene showed nucleotide and deduced amino acid identities ranged from 76.8 to 100% and 86.4 to 100%, respectively. Phylogenetic analysis showed that all isolates of SMYEV fell into four clades. To a certain extent, the clades were related to the geological distribution of SMYEV. Isolates SY02 and SY03, derived from Fragaria pentaphylla and F.xananassa cv. Changhong 2, respectively, had a far relationship with other isolates and fell into one clade. They were likely to be the special isolates that only existed in China. The 3' untranslated region (UTR) of SMYEV RNA was predicted to contain four stem-loop structures. RNA secondary structure analysis of the 3' UTR of 28 SMYEV isolates revealed that the isolates fell into three distinct groups. It was related to the clustering of isolates as resulting from phylogenetic analysis. Several optimal and sub-optimal forms of 3' UTR of potexviruses with lowest free-energy secondary structure were predicted. The conserved hexannucleotide motif and characteristic of secondary structure of potexviruses were also analyzed.