Zou Wen-Chao, Shen Lin-Lin, Shen Jian-Guo, Cai Wei, Zhan Jia-Sui, Gao Fang-Luan
Institute of Plant Virology, Fujian Agriculture and Forestry University/Key Laboratory of Plant Virology of Fujian Province, Fuzhou 350002, China.
Inspection & Quarantine Technology Center of Fujian Entry-Exit Inspection and Quarantine Bureau/Fujian Key Laboratory for Technology Research of Inspection and Quarantine, Fuzhou 350001, China.
Yi Chuan. 2017 Oct 20;39(10):918-929. doi: 10.16288/j.yczz.17-206.
The objective of this study is to develop a rapid and accurate multigene phylogenetic analysis to identify Potato virus Y (PVY) strains. The phylogenetic relationships of strains within the PVY species were evaluated with isolate-strain association using five datasets of concatenated sequences from the P1, HC-pro, VPg and CP genes to determine the best dataset for PVY strain identification. Results from phylogenetic analyses and Bayesian tip-association significance (BaTS) tests indicated that the major PVY strains could be distinguished using the P1, VPg and CP concatenated sequences datasets but not the remaining concatenated sequence datasets. Phylogenetic trees reconstructed from the concatenated sequences of P1, VPg and CP genes revealed that the ML and NJ trees had broadly similar topologies and that both were better than the maximum clade credibility tree (MCC). Additionally, the full genome of HLJ26, one isolate randomly selected for the multigene phylogenetic analysis, was clustered with high confidence among members of the PVY (SYR-Ⅱ) strain, which includes isolates of SYR-Ⅱ-2-8, SYR-Ⅱ-Be1 and SYR-Ⅱ-DrH. This suggests that it was a PVY (SYR-Ⅱ) isolate. Recombination analysis of this isolate identified four putative recombination joints in the P1, HC-pro/P3, VPg and the 5'-terminus of CP. This pattern is similar to that observed in the genomic structure of PVY (SYR-I), supporting the classification of this isolate as the PVY strain (SYR-Ⅱ). Simultaneously, two expected fragments of approximately 1 000 and 400 bp in size were also amplified from the isolate by a multiplex RT-PCR, consistent with the expected band pattern of the PVY (SYR-Ⅱ) strain. This further supports the utility of the multigene phylogenetic method in identifying PVY strains. We propose that the major PVY strains could be distinguished accurately using multigene phylogenetic analysis based on the concatenated sequences from the P1, VPg and CP genes.
本研究的目的是开发一种快速准确的多基因系统发育分析方法，以鉴定马铃薯Y病毒（PVY）株系。利用来自P1、HC-pro、VPg和CP基因的五个串联序列数据集，通过分离株-株系关联评估PVY物种内株系的系统发育关系，以确定用于PVY株系鉴定的最佳数据集。系统发育分析和贝叶斯末端关联显著性（BaTS）测试结果表明，使用P1、VPg和CP串联序列数据集可以区分主要的PVY株系，但不能区分其余的串联序列数据集。从P1、VPg和CP基因的串联序列重建的系统发育树表明，最大似然法（ML）树和邻接法（NJ）树具有大致相似的拓扑结构，且两者均优于最大分支可信度树（MCC）。此外，随机选择用于多基因系统发育分析的一个分离株HLJ26的全基因组，在PVY（SYR-Ⅱ）株系成员中高度可信地聚类，该株系包括SYR-Ⅱ-2-8、SYR-Ⅱ-Be1和SYR-Ⅱ-DrH分离株。这表明它是一个PVY（SYR-Ⅱ）分离株。对该分离株的重组分析在P1、HC-pro/P3、VPg和CP基因的5'-末端鉴定出四个假定的重组位点。这种模式与在PVY（SYR-I）基因组结构中观察到的模式相似，支持将该分离株分类为PVY株系（SYR-Ⅱ）。同时，通过多重逆转录聚合酶链反应（multiplex RT-PCR）也从该分离株中扩增出两个预期大小约为1000和400 bp的片段，与PVY（SYR-Ⅱ）株系的预期条带模式一致。这进一步支持了多基因系统发育方法在鉴定PVY株系中的实用性。我们建议基于P1、VPg和CP基因的串联序列，使用多基因系统发育分析能够准确区分主要的PVY株系。
