Molecular detection, and partial nucleotide sequencing of Cassava common mosaic virus on pistachio in Iran

The pistachio is a semitropical dioecious tree cultivated primarily for its nuts. Despite its agricultural significance, comprehensive screening for plant virus diseases affecting pistachios has been lacking. This study undertakes a bioinformatic analysis of published transcriptomic datasets from the Sequence Read Archive (SRA) within the NCBI database, specifically focusing on samples from Kerman province, to identify potential viral agents that may infect pistachio trees.

Transcriptomic data were aligned with the Pistachio vera reference genome to filter out plant RNAs. The resulting sequences were assembled into a contiguous format, refined, and subsequently compared with NCBI GenBank using a BLASTn search. To explore the phylogenetic relationships of the virus, multiple sequence alignments were conducted based on the complete genomic sequences, as well as the replicate and coat protein open reading frames (ORFs).

Bioinformatic analysis identified a member of the potexviruses in a pistachio sample. The genomic RNA sequence of an isolate (Pis), consisting of 4635 nucleotides, was determined. The virus genome is structured with five open reading frames and includes the complete 3' untranslated region (3' UTR), the coat protein gene, a triple gene block (TGB), and a partial RNA-dependent RNA polymerase (RdRp), reflecting the typical arrangement found in members of the genus Potexvirus. Sequence alignment and nucleotide BLAST analysis indicated that the Pis isolate shares 88% to 94% identity with the complete genome sequence of Cassava common mosaic virus (CsCMV) isolates.

According to the sequence and phylogenetic analysis, the pistachio isolate of CsCMV was closely related to other CsCMV isolates. This is the first report of CsCMV in P. vera.