Abstract
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.
Funder
Russian Science Foundation
Subject
Molecular Biology,Biochemistry
Reference101 articles.
1. Bacteriophage Taxonomy: An Evolving Discipline;Tolstoy;Methods Mol. Biol.,2018
2. Turner, D., Kropinski, A.M., and Adriaenssens, E.M. (2021). A Roadmap for Genome-Based Phage Taxonomy. Viruses, 13.
3. The New Scope of Virus Taxonomy: Partitioning the Virosphere into 15 Hierarchical Ranks;Gorbalenya;Nat. Microbiol.,2020
4. Common Ancestry of Herpesviruses and Tailed DNA Bacteriophages;Baker;J. Virol.,2005
5. Current ICTV (2022, November 09). Taxonomy Release|ICTV. Available online: https://ictv.global/taxonomy.
Cited by
6 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献