Estrutura genética de populações dos begomovírus Tomato mottle leaf curl virus infectando tomate (Solanum lycopersicum) e Sida mottle Alagoas virus em Sida spp. no Brasil

Abstract

Tomato (Solanum lycopersicon) is an important crop in tropical and subtropical regions. Begomoviruses are among the most damaging pathogens infecting this crop, being considered limiting factor in tomato fields. Begomoviruses are whitefly-transmitted, single-stranded DNA plant viruses, with wild/non-cultivated hosts playing a crucial epidemiological role, acting as begomovirus reservoirs. Recently, it has been shown that Brazilian begomoviruses infecting tomatoes are biogeographically segregated, with different viral species being prevalent in different tomato-growing areas. The present study aimed to determine the diversity and genetic structure of begomovirus populations infecting tomato and Sida spp. In different tomato fields in northeastern Brazil. Foliar samples of tomato and Sida spp. Near tomato fields were collected in three different states in northeastern Brazil in 2014. Total DNA was extracted and used as a template for rolling-circle amplification of begomovirus genomes. These genomes were cloned and sequenced commercially by primer walking. To properly assign taxonomy to the novel isolates, full-length genome pairwise comparisons with previously reported begomoviruses was used. Multiple sequence alignments were prepared for the full-length DNA-A, and for the CP and Rep coding sequences of each viral species. Phylogeny, genetic variability, recombination and selection pressure analyses were performed. A total of 30 clones of DNA-A genomic component was 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. plants. Bayesian phylogenetic trees showed that ToMoLCV and SiMoAlV isolates were structured according to geographical region, which was confirmed by high Fst values [Fst(ToMoLCV) = 0.51 and Fst(SiMoAlV) = 0.75]. ToMoLCV and SiMoAlV populations showed high genetic variability, with the Rep gene of ToMoLCV being the most variable. Recombination events were detected only among ToMoLCV isolates, with recombination breakpoints occurring in the Common Region and Rep. Negative or purifying selection was identified as the major selective force acting on CP and Rep in both ToMoLCV and SiMoAlV. The present study confirmed that ToMoLCV is the main begomovirus infecting tomato plants in northeastern Brazil, and showed that Sida spp. seems do not contribute to ToMoLCV outbreaks in tomato.