A novel badnavirus discovered in Fig tree by high-throughput sequencing

Abstract A novel plant virus was detected in the ring spot symptomatic fig leaves by high-throughput sequence (HTS). The virus has a circular DNA genome, with a full length of 7233 (nt), and contains four open reading frames (ORFs). ORF1 and ORF2 encode a hypothetical protein, ORF3 encodes a putative polyprotein with conserved domains, including zinc finger, aspartic protease, reverse transcriptase (RT), and RNase H domains, and ORF4 encodes a putative protein of unknown function. Based on the RT+RNase H region nucleotide sequence pairwise comparisons showed that FBV-2 shares 84.46% and 78.82% sequence identity with Grapevine badnavirus 1 (MF781082.1) and Fig badnavirus 1(MK348055.1). Interestingly FBV-2 has genome organization differences in GBV-1, but not with FBV-1, and phylogenetic analysis showed FBV-2 three isolates were clustered separately in a group and formed a branch of badnavirus. Genome organization and phylogenetic analysis display that the novel virus is a new member of the genus Badnavirus and is tentatively named “Fig badnavirus 2” (FBV-2).