Abstract
Plants of okra, marigold, pineapple, neem, datura, duranta, mirabilis, pedilanthus, helichrysum, and castor exhibiting various symptoms were collected from different locations in Karnataka (India). To confirm begomovirus infection, PCR amplification was performed on 45 symptomatic samples from various crops using begomovirus-specific primers. The complete genomes of chilli leaf curl virus (ChLCuV) and its associated betasatellite were successfully amplified, cloned, and sequenced from all ten affected crops. SDT analysis of the DNA-A segment from the ten ChLCuV-infected crops revealed distinct nucleotide identity patterns were observed. For instance, the okra isolate showed high homology with ChLCuV (99% nucleotide identity), while isolates from neem, marigold, castor, helichrysum, pineapple, and datura exhibited maximum nucleotide identity with chilli leaf curl Ahmedabad virus (ChLCuAV). In addition, isolates from pedilanthus, duranta, and mirabilis showed over 91% nucleotide identity with chilli leaf curl India virus (ChLCINV), previously reported in chilli from India and Oman. Moreover, the betasatellite amplified from pineapple, helichrysum, datura, okra, neem, pedilanthus, castor, mirabilis, and marigold showed over 95% nucleotide identity with several isolates of tomato leaf curl Bangladesh betasatellites (ToLCBDB). RDP analysis of the viral genome and betasatellites indicated significant recombination, suggesting that the begomoviruses infecting these ten diverse host species have evolved through genetic exchanges with pre-existing begomoviruses. Furthermore, a LAMP assay was developed and successfully detected begomovirus infections in symptomatic samples from all ten crops, demonstrating its potential as a rapid and reliable diagnostic tool for field-level detection. This is the first report of ChLCuV, ChLCuAV, ChLCINV and betasatellites infecting okra, marigold, pineapple, neem, datura, duranta, mirabilis, pedilanthus, helichrysum, and castor in India. Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04434-y.