College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
College of Plant Protection, Yangzhou University, Yangzhou 225009, China.
Genes (Basel). 2023 Aug 28;14(9):1712. doi: 10.3390/genes14091712.
Prunus necrotic ringspot virus (PNRSV) is a significant virus of ornamental plants and fruit trees. It is essential to study this virus due to its impact on the horticultural industry. Several studies on PNRSV diversity and phytosanitary detection technology were reported, but the content on the codon usage bias (CUB), dinucleotide preference and codon pair bias (CPB) of PNRSV is still uncertain. We performed comprehensive analyses on a dataset consisting of 359 coat protein (CP) gene sequences in PNRSV to examine the characteristics of CUB, dinucleotide composition, and CPB. The CUB analysis of PNRSV sequences showed that it was not only affected by natural selection, but also affected by mutations, and natural selection played a more significant role compared to mutations as the driving force. The dinucleotide composition analysis showed an over-expression of the CpC/GpA dinucleotides and an under-expression of the UpA/GpC dinucleotides. The dinucleotide composition of the PNRSV gene showed a weak association with the viral lineages and hosts, but a strong association with viral codon positions. Furthermore, the CPB of PNRSV gene is low and is related to dinucleotide preference and codon usage patterns. This research provides reference for future research on PNRSV genetic diversity and gene evolution mechanism.
李坏死环斑病毒（PNRSV）是一种重要的观赏植物和果木病毒。由于其对园艺产业的影响，研究该病毒至关重要。已经有一些关于 PNRSV 多样性和植物检疫检测技术的研究报告，但关于 PNRSV 的密码子使用偏性（CUB）、二核苷酸偏好和密码子对偏性（CPB）的内容仍不确定。我们对包含 359 个外壳蛋白（CP）基因序列的数据集进行了综合分析，以研究 CUB、二核苷酸组成和 CPB 的特征。PNRSV 序列的 CUB 分析表明，它不仅受到自然选择的影响，还受到突变的影响，并且自然选择比突变作为驱动力发挥更重要的作用。二核苷酸组成分析显示 CpC/GpA 二核苷酸表达过度，UpA/GpC 二核苷酸表达不足。PNRSV 基因的二核苷酸组成与病毒谱系和宿主有弱相关性，但与病毒密码子位置有强相关性。此外，PNRSV 基因的 CPB 较低，与二核苷酸偏好和密码子使用模式有关。这项研究为未来研究 PNRSV 遗传多样性和基因进化机制提供了参考。
