Ranavirus,轮状病毒科内Ranavirus属的成员,已经成为全球两栖动物种群的一个重要问题,以及其他冷血脊椎动物,由于它们作为重大威胁而出现。我们使用生物信息学工具来检查来自Ranavirus的61DNApol基因中的密码子使用模式,淋巴细胞病毒,巨细胞病毒,还有两种未分类的病毒,因为之前没有关于这个主题的研究。结果表明,Ranavirus的DNApol基因中存在轻微或低水平的密码子使用偏差(CUB)。相对同义密码子使用(RSCU)分析表明,在RanavirusDNApol基因中偏爱的主要密码子终止于C或G。检查核苷酸含量的相关分析,第三密码子位置,有效密码子数(ENC)对应分析(COA),香气值,和GRAVY值表明,跨DNApol基因的CUB可能受到突变压力和自然选择的影响。中性图表明自然选择是驱动密码子使用的主要因素。此外,密码子适应指数(CAI)的分析表明RanavirusDNApol基因对其宿主的强大适应性。对相对密码子去优化指数(RCDI)的分析表明,RanavirusDNApol基因受到其宿主更大的选择压力。这些发现将有助于理解影响Ranavirus对其宿主的进化和适应的因素。
Ranaviruses, members of the genus
Ranavirus within the family Iridoviridae, have become a significant concern for amphibian populations globally, along with other cold-blooded vertebrates, due to their emergence as a significant threat. We employed bioinformatics tools to examine the codon usage patterns in 61 DNA pol genes from
Ranavirus, Lymphocystivirus, Megalocytivirus, and two unclassified ranaviruses, as no prior studies had been conducted on this topic. The results showed a slight or low level of codon usage bias (CUB) in the DNA pol genes of
Ranavirus. Relative synonymous codon usage (RSCU) analysis indicated that the predominant codons favored in
Ranavirus DNA pol genes terminate with C or G. Correlation analysis examining nucleotide content, third codon position, effective number of codons (ENC), correspondence analysis (COA), Aroma values, and GRAVY values indicated that the CUB across DNA pol genes could be influenced by both mutation pressure and natural selection. The neutrality plot indicated that natural selection is the primary factor driving codon usage. Furthermore, the analysis of the codon adaptation index (CAI) illustrated the robust adaptability of Ranavirus DNA pol genes to their hosts. Analysis of the relative codon deoptimization index (RCDI) suggested that Ranavirus DNA pol genes underwent greater selection pressure from their hosts. These findings will aid in comprehending the factors influencing the evolution and adaptation of
Ranavirus to its hosts.