A novel phylogenetic lineage clustered by NIa gene of Sugarcane streak mosaic virus Yunnan isolates

Abstract:

[Objective] We assessed the phylogenetic relationship of Sugarcane streak mosaic virus (SCSMV) according to NIa sequences, to infer the prevalence and variation of SCSMV and to prevent and control this virus.[Methods] Leaf samples with mosaic symptom were collected from sugarcane-growing areas in Yunnan province and the Chinese national nursery of sugarcane germplasm resources (NNSGR). NIa sequences of SCSMV were determined by RT-PCR, and analyzed by Splits Tree, RDP, PhyML and DnaSP softwares, in aspect of phylogenetic, selection, and gene flow.[Results] We obtained 23 NIa sequences; clear recombination site was not found in NIa; a novel cluster formed by SCSMV Yunnan isolates determined here was found; strong purifying selection was found in NIa of SCSMV; and the gene flow of SCSMV subpopulations between sugarcane-growing areas in Yunnan province and the NNSGR was not frequent.[Conclusion] Similar with P1, HC-Pro and CP genes, SCSMV isolates could be divided into five clusters. NIa of SCSMV Yunnan isolates showed high genetic diversity and clear geographical distribution.