Phylogenetic analysis of two Iranian grapevine virus A isolates using coat protein gene sequence

Symptomatic grapevine samples were collected from vineyards in Zanjan province to detect Grapevine virus A. Total RNA was extracted from symptomatic leaf samples and subjected to cDNA synthesis using random hexamer primers. Then, a DNA fragment around ۸۰۰ bp including the complete coat protein (CP) gene was amplified from nine out of ۵۷ samples by polymerase chain reaction (PCR) using specific primers. The infection rate of GAV in vineyards was around ۴%, ۶%, ۲%, and ۶% in Zanjan, Abhar, Tarom, and Khoramdareh, respectively. Two DNA fragments corresponding to samples Abhar (p۲۵) and Zanjan (p۲۶), were purified and sequenced. The CP-nucleotide sequence identity between two Iranian isolates was ۹۷.۳%. However, sequence identity with previously reported isolates were ۷۶ to ۹۵% and ۸۲ to ۹۸% at the nt and amino acid levels, respectively. CP-based phylogenetic trees showed three main groups (I, II, III) in which p۲۵ (MG۹۷۷۰۱۳) and p۲۶ (MG۹۷۷۰۱۳) isolates were placed in the group I together with isolates from different geographical regions including Palestine (Israel), Italy, Czech Republic, Jordan, USA and South Africa. To our knowledge, this is the first report of detection and phylogenetic analysis of GVA isolates from Iranian vineyards based on the complete CP gene. Positive selection value was observed on codon ۲۵ indicating the role of this position probably in virus survival and flexibility against evolutionary forces.

Keywords:

Coat protein , Phylogenetic analysis , RT-PCR , Sequencing , Vitivirus