Genetic Diversity and Evolutionary Dynamics of Begomoviruses Reported from Sri Lanka

Abstract

Begomoviruses, members of the family Geminiviridae, pose a major challenge to crop production in Sri Lanka and globally due to their extensive host range and high evolutionary potential. This study investigated the genetic diversity and evolutionary dynamics of begomoviruses reported from Sri Lanka using publicly available genomic sequences. Viral sequences were retrieved from the NCBI database and aligned using MUSCLE. Pairwise sequence identity was assessed using SDT (v1.2), while phylogenetic relationships, nucleotide diversity, and selection pressure analyses were conducted using MEGA version 12. Recombination events were detected using RDP4 employing multiple algorithms. The analysis revealed four major begomovirus groups based on sequence identity and phylogenetic clustering: Okra enation leaf curl virus (OELCuV), Bhendi yellow vein mosaic virus (BYVMV), Sri Lankan cassava mosaic virus (SLCMV), and Tomato leaf curl Sri Lankan virus (ToLCSLV). Phylogenetic analysis supported clear species level segregation with strong bootstrap confidence. Five recombination events were identified, indicating active genetic exchange among begomovirus populations. Selection pressure analysis showed that most viral genes are under strong purifying selection, suggesting evolutionary conservation, whereas limited evidence of positive selection was observed in specific genes. Nucleotide diversity varied among populations, with OELCuV isolates exhibiting the lowest diversity, indicating a more conserved genome compared to other groups. Overall, this study highlights the significant genetic diversity and ongoing evolution of begomoviruses in Sri Lanka, emphasizing the role of recombination and selection in shaping viral populations and their potential impact on crop health and management strategies.