Genome characterization of chili leaf curl virus, the associated alphasatellite and betasatellite and demonstration of pathogenesis of the virus in south-eastern Iran

Begomovirus infecting vegetables is one of the main components of yield losses in south-eastern Iran. In this study, the incidence of chili leaf curl virus (ChiLCV) and the associated satellites were studied in pepper farms and commercial greenhouses of Jiroft and Manoojan (Kerman province). Full-length genome of three ChiLCV isolates was amplified using the rolling circle amplification method followed by cloning and sequencing. Furthermore, associated alpha- and betasatellites genomes were amplified in the PCR assay using specific and degenerate primer pairs, respectively. Sequence comparison showed that three ChiLCV isolates shared >95% pairwise nucleotide identities with the selected GenBank isolates. Gossypium darwinii symptomless alphasatellite (GDarSLA) was also found to be associated with three ChiLCV isolates and shared >89% pairwise identities with the selected GenBank isolates. Furthermore, tomato leaf curl betasatellie (ToLCB) was identified in two pepper isolates from Manoojan and shared >94% pairwise identities with the selected GenBank isolates. To demonstrate the pathogenesis of ChiLCV, a partial dimer of the viral genome was designed, constructed and agroinoculated into pepper seedlings. This led to the appearance of typical ChiLCV symptoms, including dwarfing and yellowing. Collectively, ChiLCV is one of the important begomoviruses infecting pepper in south-eastern Iran and the full-length genome of the virus as well as the associated alphasatellite are reported for the first time in Iran.