Molecular variability of Tobacco vein banding mosaic virus populations

The incidence of Tobacco vein banding mosaic virus (TVBMV) on tobacco increases dramatically in China recently and it has caused great economic losses. To gain insights into the evolutionary mechanisms of TVBMV, a total of 40 TVBMV isolates were collected from different tobacco production regions in China and their genomic regions encoding helper component-proteinase (HC-Pro), the third protein (P3), the first 6K protein (6K1) and coat protein (CP) were sequenced. Phylogenetic analyses revealed that TVBMV isolates can be divided into two evolutionary divergent groups based on P3, the frame-shifting pipo and 6K1 genes, and three groups on HC-Pro and CP genes. The populations from most parts of mainland China (MC) showed frequent gene flow; those from Yunnan province in south western China always formed a separate group (YN) and also had frequent within-group gene flow. However, the gene flow between groups MC and YN was uncommon. Our results revealed that all the tested TVBMV genes were under negative selection and the HC-Pro gene was under the strongest constraints. Recombination events were identified in 13 of the 42 analyzed isolates. This study suggested that negative selection, gene flow and recombination were important evolutionary factors driving the genetic diversification of TVBMV.