Metagenomic Analysis of Malva sylvestris from Iran Displays a Malva Vein Clearing Virus Genome

To date, only the complete genome of one malva vein clearing virus (MVCV) has been sequenced worldwide. Here, for the first time, the genomic sequence of an isolate of MVCV affecting Malva sylvestris in Iran was determined, using RNA deep sequencing confirmed by reverse-transcription polymerase chain reaction and Sanger sequencing. The sequence of IR۱ was ۱۱,۰۵۵ nucleotides in length and contained a single open reading frame of ۱۰,۵۲۷ nucleotides encoding a large polyprotein of ۳,۵۰۸ amino acids with predicted molecular weight of ۳۹۵,۰۸ KDa. The sequence contained nine putative proteolytic cleavage sites and motifs conserved in homologous proteins of other potyviruses. The P۱ of the IR۱ was ۱۲۳۶ nucleotides longer than that of the only recently reported sequence from China (MVCV-SX, MN۱۱۶۶۸۳). The complete genome sequence obtained from the study showed ۸۱.۲۴% and ۹۱.۹۳% identities to its Chinese counterpart at the nucleotide (nt) and deduced amino acid (aa) levels, respectively. The low nt and aa sequence identity with known MVCV isolate seems to indicate that IR۱ is a novel strain. Phylogenetic analysis of the coat protein gene also showed that the Iranian isolate was most closely related to the Dutch isolate NAKT-NL (FJ۵۳۹۰۸۴), with identities of ۹۴.۰۶ (at nt level) and ۹۶.۰۴% (at aa level). The results of this study will be useful for understanding the global molecular epidemiology of MVCV.

Keywords:

Complete genome , High-throughput sequencing , MVCV.