云南蔗区甘蔗线条花叶病毒分离物NIa基因形成新簇

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

摘要:

[目的] 利用NIa基因，阐明甘蔗线条花叶病毒（Sugarcane streak mosaic virus，SCSMV）的种系发生关系，为预测SCSMV流行变异趋势及科学防控提供理论依据。[方法] 从云南蔗区和国家甘蔗种质资源圃采集感病样品，RT-PCR扩增获得SCSMV NIa基因序列后，使用Splits Tree、RDP、PhyML、DnaSP等软件分析SCSMV中国分离物的系统发生、选择压力及基因流动等特征。[结果] 共获得23条SCSMV NIa基因序列。这些序列间未发生重组，云南蔗区的部分序列形成1个新簇，且云南蔗区与国家甘蔗种质资源圃之间的基因交流不显著。此外，选择压力分析表明，NIa基因受很强的负选择压力作用。[结论] 与P1、HC-Pro和CP等基因类似，SCSMV在NIa基因上也包含5个簇；SCSMV云南分离物具有较高的遗传多样性和清晰的地理相关性。

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.