The Complete Genome Sequences of Two Recombinant Isolates of Squash Mosaic Virus from Iran

Squash Mosaic Virus (SqMV) is a Comovirus that infects many cucurbit crops worldwide. In this study, the first two complete genome sequences of SqMV (BSQ and TSQ) from Iran were determined. The RNA genomes of isolates BSQ and TSQ were, respectively, ۵,۷۵۴ and ۵,۷۵۵ (RNA۱) and ۳۲۹۰ and ۳۲۷۱ (RNA۲) nucleotides (nt) in length, excluding the ۳'-terminal poly (A) tail. RNA۱ of both isolates encodes a single polyprotein of ۱۸۵۸ amino acids (aa). The identity between the two Iranian isolates (BSQ and TSQ) was ۹۴.۲۴% nt and ۹۴.۸۲% aa for RNA۱ and ۸۸.۸۰% nt and ۸۹.۵۰% aa for RNA۲. In comparison to other SqMV isolates, BSQ and TSQ shared the highest nucleotide sequence identities of ۹۵.۱۲ % to ۹۳.۵۶ % (RNA۱), and ۸۷.۵۹ % to ۸۷.۱۹ % (RNA۲), respectively, with the Spanish isolate (RZ-SqMV). Phylogenetic analysis based on complete genome sequences reveals that SqMV isolates cluster into three distinct groups. BSQ was clustered alongside a Spanish isolate in one group and TSQ was separately clustered with a Chinese and US isolates in another group. Recombination analysis revealed that BSQ (RNA۱, ۲) and TSQ (RNA۲) were putative recombinants. BSQ had ۶ recombination sites within ۵'-UTR, helicase, protease, RdRP (in RNA۱), SCP and ۳'-UTR (in RNA۲) regions, whereas TSQ had ۴ recombination sites within ۵'-UTR, MP (two breaking points) and LCP region.

کلیدواژه ها:

Comovirus ، Cucurbits ، Phylogenetic analysis ، Recombination ، SqMV.