Genetic structure of populations of the begomoviruses Tomato mottle leaf curl virus and Sida mottle Alagoas virus infecting tomato (Solanum lycopersicum) and Sida spp., respectively

Begomoviruses are among the most damaging pathogens infecting cultivated hosts worldwide, and are considered an important limiting factor in tomato fields. In the present study, foliar samples of tomato and Sida spp. were collected in Boqueirão, state of Paraíba, Brazil, in May 2014. Viral genomes were amplified, cloned and sequenced. A total of 30 DNA-A components were obtained. Pairwise comparisons indicated the presence of only two begomovirus species: Tomato mottle leaf curl virus (ToMoLCV) from tomato samples and Sida mottle Alagoas virus (SiMoAV) in Sida spp. ToMoLCV and SiMoAV subpopulations showed high genetic variability, with the ToMoLCV Rep gene being the most variable. Recombination events were detected only among ToMoLCV isolates, with recombination breakpoints occurring in the common region and in the Rep gene. Negative or purifying selection seems to be among the most important evolutionary mechanisms acting on the CP and Rep genes in both ToMoLCV and SiMoAV. Our results indicate that ToMoLCV remains as the main tomato-infecting begomovirus in northeastern Brazil, and that Sida spp. do not contribute to ToMoLCV epidemics in tomato.