In silico identification of two novel viruses on Iranian pistachio

The pistachio is a commercial nut crop that belongs to the family Anacardiaceae. Reports for viral agents of this plant are limited to hop stunt viroid, pistachio ampelovirus A, and pistacia virus B. We investigated of the presence of viruses in Iranian Pistacia vera by analyzing publicly available RNA-Seq data. Twelve paired-end datasets were retrieved from the Sequence Read Archive (SRA) database of NCBI. Transcriptomic data were mapped to P. vera reference genome using Hisat2 to eliminate plant RNAs. The remaining data were de novo assembled by MEGAHIT and Trinity programs and the resultant contigs subsequently were queried versus viral reference sequences using BLASTx. Two novel viruses related to the family Kitaviridae were identified and tentatively named “pistachio virus x” (MT334618-20) and “pistachio virus y” (MT362605-06). Based on the genome structure, sequences similarity, and phylogenetic relationships we propose these novel viruses as possible members of genera Higrevirus and Cilevirus. High reads number on different plant tissues, root and leaf, of pistachio virus x led us to make a conclusion on possible systemic infection of this virus on Pistacia vera. To the best of our knowledge, it is the first report of possible viral agent from Iranian pistachios.