Detection, phylogenetic and population genetic analysis of Apple stem grooving virus based on coat protein gene

Apple stem grooving virus (ASGV) is one of the important viruses infecting apple trees. In this research, 87 symptomatic and symptomless leaf and bark samples were collected from the apple orchards in west and south west of Zanjan and east of Kurdistan provinces to detect ASGV. After total RNA extraction from 50 out of 87 samples, cDNAs were synthesized by reverse primer and PCR optimized using a pair of specific primer corresponding to complete coat protein gene. A DNA segment with 728 bp length corresponding to complete coat protein gene was amplified from twelve samples by RT-PCR. Nine PCR-products including four samples cloned into pTG19 and five samples without cloning were sequenced. The sequencing and blast results revealed that the fragments belong to coat protein gene of Apple stem grooving virus. Phylogenetic analysis of new Iranian isolates and those retrieved from GenBank by MEGA 7 and Neighbor-Joining methods in Jukes-Cantor model showed that the new Iranian isolates were placed in a sub-clade with reported Iranian, Indian, South Korean and Chinese isolates. The result revealed that the least dN/dS ratio belonging to Iranian isolates and the most gene flow was calculated between isolates from Iran, China and South Korean. This is the first report of Apple stem grooving virus from the Zanjan region.