Detection and Molecular Characterization of Fig badnavirus-1 Iranian isolates on the Basis of the Protease Gene

Fig badnavirus-1, a species of the genus Badnavirus in the family Caulimoviridae, is one the most prevalent viruses associated with the fig mosaic disease through in fig plantations worldwide. During the growing seasons of the year 2012-2013, a total of 392 asymptomatic and symptomatic leaf samples were collected from different fig orchards located in 9 provinces of Iran. Using the DIBA serological test and universal serum, samples were tested for the presence of fig mosaic disease. Following total DNA extraction from infected samples, an amplicon with a size about 1055bp was amplified using specific primer for FBV-1 protease gene. RFLP test was conducted with the PCR products of the FBV-1 infected samples and EcoRI enzyme to assess the genetic variation of infected isolates. Protease gene of nine representative FBV-1 samples from different provinces were sequenced and submitted in GenBank under the accession numbers KU314932-40. Blast analysis showed 98-99% identity between the Iranian isolates at the nucleotide and amino acid levels. Phylogenetic analysis on the basis of the nucleotide sequences of studied isolates categorized them into two different groups in which Iranian isolates grouped together in a separate group distinct from American isolate. Phylogeny on the basis of the amino acid sequence revealed a different phylogenetic tree. Totally, results of this study indicated the presence of different FBV-1 populations in Iran.