Genetic diversity and evolution of Tomato spotted wilt virus (TSWV)
Tsompana M1, Carbone I2, Abad J3, Moyer JW3
1Department of Plant Pathology, University of North Carolina-Chapel Hill, Chapel Hill, NC
2Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC
3Department of Plant Pathology, North Carolina State University, Raleigh, NC
Correspondence: mtsompa@ncsu.edu
Tomato spotted wilt virus (TSWV) is a leading plant viral pathogen (Moyer JW 1999. In: Webster R, Granoff, A, editors. Encyclopedia of Virology, 1803每7. Academic Press; Moyer JW. 2000. In: Hull R, editor, Encyclopedia of Microbiology, 592每597: Academic Press; Tsompana M et al. 2005. Molecular Ecology 14: 53每66) that infects more than 900 plant and 10 thrips species. TSWV has been shown to adapt to selection pressures by reassortment (Qiu WP et al. 1998. Virology 244: 186每194) and by accumulation of defective mutants in the population (Sin SH et al. 2005. Proceedings of the National Academy of Sciences USA 102: 5168每5173). The overall goal of this study was to elucidate the molecular evolution and population genetics of TSWV, at the species level and within individual isolates. Initially, to characterize the recent evolutionary history of the TSWV species we used consensus sequence data from genes encoding five viral proteins. Our analysis provided the first demonstration of population structuring and species-wide population expansions for TSWV, attributed to founder effects (Tsompana et al. 2005. Molecular Ecology 14: 53每66; Tsompana et al. 2003. Phytopathology 93. Supplement 6: 84). We also identified positive selection favoring divergence between Tospovirus species and purifying selection acting at the species level to preserve protein function. Subsequently, analyses of thirteen individual TSWV isolates (represented by 516 clones) revealed that natural TSWV isolates are highly heterogeneous viral populations that consist of one or two haplotypes with high frequency and an array of closely related rare haplotypes, some of which have deletions and/or stop codons. These viral populations exhibit a high transitional bias, related to the function of RdRp polymerase or dsRAD. Analysis based on tests of neutrality, gene genealogies and the coalescent uncovered a population history of genetic bottlenecks followed by population growth for all viral isolates, and a limited amount of recombination for three viral isolates. Migration was significantly restricted between viral populations. Overall, our findings improve our knowledge on the important factors that govern the evolution of plant RNA viruses.
