College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, Jiangsu Province, PR China.
College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, Jiangsu Province, PR China.
Int J Biol Macromol. 2023 Jun 15;240:124403. doi: 10.1016/j.ijbiomac.2023.124403. Epub 2023 Apr 18.
Patatavirales is the largest order of plant RNA viruses and exclusively contains the family Potyviridae, accounting for 30 % of all known plant viruses. The composition bias of animal RNA viruses and several plant RNA viruses has been determined. However, the comprehensive nucleic acid composition, codon pair usage patterns, dinucleotide preference and codon pair preference of plant RNA viruses have not been investigated to date. In this study, integrated analysis and discussion of the nucleic acid composition, codon usage patterns, dinucleotide composition and codon pair bias of potyvirids were performed using 3732 complete genome coding sequences. The nucleic acid composition of potyvirids was significantly enriched in A/U. Interestingly, the A/U-rich nucleotide composition of Patatavirales is essential for determining the preferred A-ended and U-ended codons and the overexpression of UpG and CpA dinucleotides. The codon usage patterns and codon pair bias of potyvirids were significantly correlated with their nucleic acid composition. Additionally, the codon usage pattern, dinucleotide composition and codon-pair bias of potyvirids are more dependent on the classification of the virus compared with their hosts. Our analysis provides a better understanding of future research on the origin and evolution patterns of the order Patatavirales.
马铃薯病毒目是植物 RNA 病毒中最大的目，仅包含壶菌科，占所有已知植物病毒的 30%。已经确定了动物 RNA 病毒和几种植物 RNA 病毒的组成偏向性。然而，迄今为止，尚未对植物 RNA 病毒的综合核酸组成、密码子对使用模式、二核苷酸偏好性和密码子对偏好性进行研究。在这项研究中，使用 3732 个完整基因组编码序列对壶菌科的核酸组成、密码子使用模式、二核苷酸组成和密码子对偏好性进行了综合分析和讨论。壶菌科的核酸组成显著富含 A/U。有趣的是，马铃薯病毒目的 A/U 丰富的核苷酸组成对于确定首选的 A 端和 U 端密码子以及 UpG 和 CpA 二核苷酸的过度表达至关重要。壶菌科的密码子使用模式和密码子对偏好性与其核酸组成显著相关。此外，与宿主相比，壶菌科的密码子使用模式、二核苷酸组成和密码子对偏好性更多地取决于病毒的分类。我们的分析为进一步研究马铃薯病毒目的起源和进化模式提供了更好的理解。
