| Exploring the genetic diversity and evolutionary history of plant viruses is critical to understanding their ecology and epidemiology. Tomato spotted wilt virus (TSWV) is an ambisense RNA virus that infects over 1000 species of plants and has been shown to reassort its genome. To further investigate this virus, maximum-likelihood and population genetics-based methods were used to investigate the population structure, genetic diversity, and sources of genetic variation in field isolates of TSWV from peanut in North Carolina and Virginia. Selected regions of the nucleocapsid, movement, and RNA-dependent RNA polymerase genes were amplified and sequenced to identify haplotypes and infer genetic relationships between isolates of TSWV with heuristic methods. The haplotype structure of each locus consisted of one or two predominant haplotypes and more than 100 haplotypes represented by a single isolate. No specific haplotypes or clades were associated with geographic area, peanut cultivar or year. The population was panmictic at the regional level and high levels of genetic diversity were observed among isolates. There was evidence for negative selection acting upon each locus and maximum-likelihood analyses, which indicated that exponential growth was occurring in the population. The results of compatibility analyses and the persistence of specific gene sequences in isolates collected over three field seasons suggest that recombination was occurring in the population. Phylogenetic analysis supports that each locus has an independent evolutionary history.Also, high diversity in viruses has been attributed to the occurrence of recombination and mutation. To investigate recombination in TSWV, matrix compatibility and ancestral recombination methods were used to detect, quantify, and reconstruct the history of recombination in three genes of TSWV in isolates collected from three cultivars of peanut (Gregory, NC12C, and Perry) sampled in multiple years. Site commonalities among the isolates collected from different cultivars were found in each gene where the majority of the recombination appeared to be occurring. These corresponded to sequence near the 3' terminus in the N and RdRP genes and to sequence near the 5' terminus in the NSm gene. Between isolates collected from different peanut cultivars, the Gregory isolates proportionally had the most recombination occurring in the N gene and the RdRP genes, while the Perry isolates had the most recombination occurring in the NSm. Recombination rates per site estimated for the N, NSm, and RdRP genes in the NC12C isolates were 0.00934, 0.01559, and 0.00495, respectively. |
