School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
Viruses. 2022 Apr 19;14(5):846. doi: 10.3390/v14050846.
Narcissus degeneration virus (NDV), narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV), which belong to the genus of the family , cause significant losses in the ornamental value and quality of narcissus. Several previous studies have explored the genetic diversity and evolution rate of narcissus viruses, but the analysis of the synonymous codons of the narcissus viruses is still unclear. Herein, the coat protein (CP) of three viruses is used to analyze the viruses' phylogeny and codon usage pattern. Phylogenetic analysis showed that NYSV, NDV and NLSYV isolates were divided into five, three and five clusters, respectively, and these clusters seemed to reflect the geographic distribution. The effective number of codon (ENC) values indicated a weak codon usage bias in the CP coding region of the three narcissus viruses. ENC-plot and neutrality analysis showed that the codon usage bias of the three narcissus viruses is all mainly influenced by natural selection compared with the mutation pressure. The three narcissus viruses shared the same best optimal codon (CCA) and the synonymous codon prefers to use codons ending with A/U, compared to C/G. Our study shows the codon analysis of different viruses on the same host for the first time, which indicates the importance of the evolutionary-based design to control these viruses.
水仙花退化病毒（NDV）、水仙花晚季黄化病毒（NLSYV）和水仙花黄条病毒（NYSV）属于 科 属，会导致水仙花观赏价值和品质的严重损失。先前已有几项研究探索了水仙花病毒的遗传多样性和进化率，但对水仙花病毒同义密码子的分析仍不清楚。在此，我们使用三种病毒的外壳蛋白（CP）分析了病毒的系统发育和密码子使用模式。系统发育分析表明，NYSV、NDV 和 NLSYV 分离株分别分为五个、三个和五个簇，这些簇似乎反映了地理分布。有效密码子数（ENC）值表明，三种水仙花病毒 CP 编码区的密码子使用存在较弱的偏好性。ENC-plot 和中性分析表明，与突变压力相比，三种水仙花病毒的密码子使用偏好性主要受自然选择的影响。三种水仙花病毒共享相同的最佳最优密码子（CCA），并且同义密码子更倾向于使用以 A/U 结尾的密码子，而不是 C/G。我们的研究首次对同一宿主的不同病毒进行了密码子分析，这表明基于进化的设计对控制这些病毒的重要性。
