Molecular characterization of Begomovirus infecting sweet pepper in Oman

Whitefly transmitted tomato yellow leaf curl is one of the most devastating viral disease of cultivated sweet pepper (Capsicum frutescens grossum) and other vegetables in Oman. Infected sweet pepper plants showed typical begomovirus symptoms as upward leaf curling, interveinal and leaf chlorosis, and growth stunting. Begomovirus infecting sweet pepper in Oman was detected by polymerase chain reaction (PCR) using begomovirus specific degenerate primers (PAL1v1978/PAR1c496 and AV494/AC1048). Core region (74-604 bp) of coat protein gene of the begomovirus was amplified by PCR with tomato yellow leaf curl virus (TYLCV) specific degenerate primers (TycpV369/TycpC1023). Core region of coat protein gene contains highly conserved regions and is used to identify the begomovirus infecting sweet peppers. Virus identification was performed by percent sequence identity and parsimony analysis using core coat protein gene sequences of sweet pepper virus with complete genome, core region of coat protein and coat protein gene sequences from reference begomoviruses. The core region sequence identity of coat protein gene of sweet pepper virus from Oman was 92.2, 96.5, 94.0, 93.8, and 96.5% with TomGV-Lebanon, TYLCV-Guadeloupe, TYLCV-Israel, TYLCV-Kuwait, and TYLCV-Mexico, respectively. Phylogenetic trees and percent sequence identity with reference to begomoviruses permitted the identification of sweet pepper virus as TYLCV based on tree position and extent of sequence identity. Phylogenetic analysis revealed that sweet pepper tomato yellow leaf curl virus clustered with its closest relatives from Middle East regions but formed a separate strain.