Evolution and selection patterns in begomoviruses infecting Phaseolus vulgaris L.

Abstract

Begomoviruses affect Phaseolus vulgaris L. that considerably decrease yield in many bean growing areas. Their evolutionary dynamics, genetic diversity and selection patterns were investigated in this study. Complete genome sequences of begomovirus isolates from different parts of the world were retrieved from GenBank. The MEGA11 was employed to align the sequences and to select the best nucleotide substitution models. Phylogenetic clustering appeared broadly consistent with geographical origin in maximum-likelihood phylogenetic trees. Transition/transversion analysis indicated relatively higher substitution rates in AV1 and AC4 as compared with other genomic regions, most likely due to vector influence and host–virus interactions. Analysis was carried out using RDP4.1 revealed that recombination is one ofthe major factors for diversification of these viruses. Neutrality tests using DnaSP v6.12 indicated that purifying selection is a predominant force driving the evolution of these viruses. High nucleotide diversity was observed in both DNA-B and betasatellites. The role of geographical distribution, mutation, recombination and selection has been analysed and discussed in the present study. In addition, the observed genetic variability among isolates highlights the adaptive potential of begomoviruses under diverse environmental and host conditions. The findings provide valuable insights into the evolutionary mechanisms shaping Begomovirus populations and contribute to a better understanding of their emergence and spread. Such information may be useful for developing effective disease management strategies and supporting breeding programs aimed at improving resistance in common bean cultivars.