Molecular characterization and evolutionary dynamics of a mixed begomovirus infection associated with chilli leaf...

Begomoviruses are one of the most genetically diverse plant-infecting DNA viruses. They significantly limit chilli (Capsicum annuum L.) production in tropical and sub-tropical areas. Their evolution is largely influenced by recombination and mixed infections. However, the relationship between genetic diversity and selection pressure in natural populations of chilli-infecting begomoviruses remains poorly understood. We collected chilli plants showing leaf curl disease symptoms from Bargarh district, Odisha, India, and tested them for begomovirus presence. Molecular analysis showed the presence of chilli leaf curl Ahmedabad virus (ChiLCAV), tomato leaf curl Joydebpur virus (ToLCJoV), and an associated betasatellite, tomato leaf curl Joydebpur betasatellite (ToLCJoB). Recombination analysis revealed multiple statistically significant recombination events in both begomovirus genomes and the betasatellite. To assess broader patterns of genetic diversity and selection, the newly generated sequences were analysed alongside publicly available sequences retrieved from the NCBI virus database. These comparative analyses revealed high haplotype diversity and a high number of segregating sites, whilst most coding regions showed strong purifying selection, with only a small number of sites showing evidence of episodic diversifying selection. These findings indicate that mixed infections can provide opportunities for recombination and the generation of genetic variation, whereas strong purifying selection constrains changes in functionally important coding regions. The combined action of recombination and selection, therefore, appears to shape the genetic diversity and evolutionary stability of chilli-infecting begomoviruses. To the best of our knowledge, this is the first report of a mixed infection involving ChiLCAV, ToLCJoV, and ToLCJoB associated with chilli leaf curl disease in India, providing new insights into the evolutionary dynamics of begomovirus complexes infecting chilli.