Global evolutionary dynamics of CLCuD-associated Begomoviruses reveal convergent adaptation and recombination hotspots in CP, Rep, and C4

Cotton leaf curl disease (CLCuD), a most destructive viral disease of cotton, is caused by at least six different begomoviruses (family Geminiviridae ). Among these, cotton leaf curl Multan virus (CLCuMuV), cotton leaf curl Kokhran virus (CLCuKoV), and cotton leaf curl Gezira virus (CLCuGeV) predominate. Despite extensive surveillance, prevalence, and genetic studies, the evolutionary mechanisms underlying their emergence, adaptation, and global dissemination remain poorly resolved. In this study, comprehensive analyses were conducted to infer evolutionary forces, including phylogeny, genetic diversity, selection pressures, and recombination patterns, shaping the emergence of three major cotton leaf curl disease (CLCuD)-associated begomoviruses (CAB) using their full-length global genomic datasets. In phylogeny, three CABs showed geographically associated clustering, revealing the long-distance dispersal, and further resolved into regional sub-clades, showing inter-regional (localized) mixing and robust evolutionary relationships. Codon-based selection analyses revealed the predominance of purifying selection across most genomic regions; nonetheless, CP, Rep, and C4 harbored strong signals of episodic diversifying- and positive selection. Recombination analysis deemed credible recombination breakpoints in CP and Rep as major recombination hubs. Population genetic analyses showed high haplotype- and low-to-high genetic diversity in CAB populations, revealing recent population expansion in CLCuKoV but more complex or prolonged evolutionary trajectories in CLCuMuV and CLCuGeV. These findings highlight that CAB evolution is being shaped by purifying selection, differential episodic diversification, and recombination, with CP, Rep, and C4 as key regions of evolutionary changes.