Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 11012, India.
ICAR-Central Citrus Research Institute, Nagpur 440033, India.
Viruses. 2019 Apr 8;11(4):331. doi: 10.3390/v11040331.
(CTV), a member of the aphid-transmitted closterovirus group, is the causal agent of the notorious tristeza disease in several citrus species worldwide. The codon usage patterns of viruses reflect the evolutionary changes for optimization of their survival and adaptation in their fitness to the external environment and the hosts. The codon usage adaptation of CTV to specific citrus hosts remains to be studied; thus, its role in CTV evolution is not clearly comprehended. Therefore, to better explain the host⁻virus interaction and evolutionary history of CTV, the codon usage patterns of the coat protein () genes of 122 CTV isolates originating from three economically important citrus hosts (55 isolate from , 38 from , and 29 from ) were studied using several codon usage indices and multivariate statistical methods. The present study shows that CTV displays low codon usage bias (CUB) and higher genomic stability. Neutrality plot and relative synonymous codon usage analyses revealed that the overall influence of natural selection was more profound than that of mutation pressure in shaping the CUB of CTV. The contribution of high-frequency codon analysis and codon adaptation index value show that CTV has host-specific codon usage patterns, resulting in higheradaptability of CTV isolates originating from (Cr-CTV), and low adaptability in the isolates originating from (Ca-CTV) and (Cs-CTV). The combination of codon analysis of CTV with citrus genealogy suggests that CTV evolved in or other progenitors. The outcome of the study enhances the understanding of the factors involved in viral adaptation, evolution, and fitness toward their hosts. This information will definitely help devise better management strategies of CTV.
(CTV)，属于蚜传杆状病毒组，是世界上几种柑橘属植物中恶疫霉病的病原体。病毒的密码子使用模式反映了其生存和适应外部环境和宿主的进化变化。CTV 对特定柑橘宿主的密码子使用适应性仍有待研究；因此，其在 CTV 进化中的作用尚不清楚。因此，为了更好地解释 CTV 与宿主的相互作用和进化历史，对来自三个经济上重要的柑橘宿主（55 个分离株来自，38 个来自，29 个来自）的 122 个 CTV 分离株的外壳蛋白（）基因的密码子使用模式进行了研究，使用了几种密码子使用指数和多变量统计方法。本研究表明，CTV 表现出低密码子使用偏好（CUB）和更高的基因组稳定性。中性绘图和相对同义密码子使用分析表明，自然选择的总体影响比突变压力对 CUB 的影响更为深刻。高频密码子分析和密码子适应指数值的贡献表明，CTV 具有宿主特异性的密码子使用模式，导致源自（Cr-CTV）的 CTV 分离株具有更高的适应性，而源自（Ca-CTV）和（Cs-CTV）的分离株适应性较低。将 CTV 的密码子分析与柑橘系谱相结合表明，CTV 是在或其他的祖先中进化而来的。该研究结果增强了对病毒适应、进化和适应宿主的因素的理解。这些信息必将有助于制定更好的 CTV 管理策略。
