Molecular characterization to study the genetic diversity of begomoviruses occurring in the major chilli growing areas of Tamil Nadu state of India.

Chilli leaf curl disease (ChiLCD), which is a significant problem in chilli cultivation, is caused by begomoviruses that are transmitted by the whitefly Bemisia tabaci. This disease leads to severe impacts on crop yields. To determine the incidence of begomovirus in the chilli crop, infected chilli leaf samples exhibiting symptoms such as curling, yellowing, reduced leaf size, and overall stunted growth were collected from various districts of Tamil Nadu, namely, Coimbatore, Dharmapuri, Kancheepuram, Karur, Salem, Krishnagiri, Thoothukudi, Thiruvallur, Tiruchirappalli, Virudhunagar, Tiruvannamalai, Tenkasi, and Vellore, during the years 2018-2022. To determine the complete genome sequence of the begomoviruses, the rolling circle amplification (RCA) method was used to clone and sequence the begomovirus genomes from the chilli samples collected from various districts of Tamil Nadu. Here we characterized 17 DNA A genome sequences and 12 betasatellite sequences. BLAST results of the DNA A genome sequences revealed nucleotide identities ranging from 94.2 to 99.7% with five distinct begomovirus species of chilli, namely, chilli leaf curl Salem virus (HM007119), chilli leaf curl virus Bhavanisagar (NC_055130), chilli leaf curl Ahmedabad virus (MW795666), chilli leaf curl virus (NC_055131), and chilli leaf curl Sri Lanka virus (JN555600). BLAST results of the betasatellite sequences showed nucleotide identities of 96 to 98.8% with the tomato leaf curl Bangladesh betasatellite (MZ151286). In the present study, five distinct begomovirus species and one associated betasatellite were found to infect chilli crops in Tamil Nadu. This finding indicates a changing pattern of begomovirus occurrence in the different districts of Tamil Nadu. This study highlights the prevalence of chilli-infecting begomoviruses in the major chilli growing districts of Tamil Nadu, the identification of begomovirus species, and the significance of understanding and managing these viruses to safeguard chilli cultivation in the region.