进化关系的评估对于病毒的分类学非常重要,这是一个迅速扩大的研究领域。属于Duplodnavria领域的病毒组的分类,其中包括尾噬菌体,头尾古细菌病毒和疱疹病毒,近年来发生了许多变化,并不断改善。Duplodnaviria分类学的一项具有挑战性的任务是对高级分类单元进行分类,包括家庭和订单。此刻,50个家庭中只有17个被分配到订单中。病毒蛋白的高度分歧使病毒之间的进化关系的评估变得复杂。然而,结构预测算法的发展,包括获奖的AlphaFold,鼓励使用结构预测的结果来阐明病毒蛋白的进化史。在这项研究中,两个保守的病毒蛋白的进化关系,主要的衣壳蛋白和末端酶,代表不同的病毒,包括所有的Duplodnavria家族,已经使用AlphaFold建模进行了分析。此分析是使用结构比较和不同的系统发育方法进行的。分析的结果主要表明AlphaFold模型的高质量和使用AlphaFold预测的可能性。与其他方法一起,重建遥远病毒群之间的进化关系。根据这种综合方法的结果,已经对完善细菌和古细菌Duplodnavria群的分类学分类做出了假设,并讨论了与Duplodnavria的分类学分类有关的问题。
The evaluation of the evolutionary relationships is exceptionally important for the taxonomy of viruses, which is a rapidly expanding area of research. The classification of viral groups belonging to the realm Duplodnaviria, which include tailed bacteriophages, head-tailed archaeal viruses and herpesviruses, has undergone many changes in recent years and continues to improve. One of the challenging tasks of Duplodnaviria taxonomy is the classification of high-ranked taxa, including families and orders. At the moment, only 17 of 50 families have been assigned to orders. The evaluation of the evolutionary relationships between viruses is complicated by the high level of divergence of viral proteins. However, the development of structure prediction algorithms, including the award-winning AlphaFold, encourages the use of the results of structural predictions to clarify the evolutionary history of viral proteins. In this study, the evolutionary relationships of two conserved viral proteins, the major capsid protein and terminase, representing different viruses, including all classified Duplodnaviria families, have been analysed using AlphaFold modelling. This analysis has been undertaken using structural comparisons and different phylogenetic methods. The results of the analyses mainly indicated the high quality of AlphaFold modelling and the possibility of using the AlphaFold predictions, together with other methods, for the reconstruction of the evolutionary relationships between distant viral groups. Based on the results of this integrated approach, assumptions have been made about refining the taxonomic classification of bacterial and archaeal Duplodnaviria groups, and problems relating to the taxonomic classification of Duplodnaviria have been discussed.