Defining a Core Genome for the Herpesvirales and Exploring their Evolutionary Relationship with the Caudovirales

Abstract

The order Herpesvirales encompasses a wide variety of important and broadly distributed human pathogens. During the last decades, similarities in the viral cycle and the structure of some of their proteins with those of the order Caudovirales, the tailed bacterial viruses, have brought speculation regarding the existence of an evolutionary relationship between these clades. To evaluate such hypothesis, we used over 600 Herpesvirales and 2000 Caudovirales complete genomes to search for the presence or absence of clusters of orthologous protein domains and constructed a dendrogram based on their compositional similarities. The results obtained strongly suggest an evolutionary relationship between the two orders. Furthermore, they allowed to propose a core genome for the Herpesvirales, composed of 4 proteins, including the ATPase subunit of the DNA-packaging terminase, the only protein with previously verified conservation. Accordingly, a phylogenetic tree constructed with sequences derived from the clusters associated to these proteins grouped the Herpesvirales strains accordingly to the established families and subfamilies. Overall, this work provides results supporting the hypothesis that the two orders are evolutionarily related and contributes to the understanding of the history of the Herpesvirales.

A Roadmap for Genome-Based Phage Taxonomy

“…As the number of phage genomes in databases rose, it quickly became apparent that these three families were not monophyletic and cohesive within a monophyletic order. This paraphyly was illustrated by a number of tools and publications: The Phage Proteomic Tree [ 10 , 11 ], the first phage genome relatedness network representation [ 12 ], a bipartite network of shared genes [ 13 ], an updated network of shared predicted proteins (vConTACT) [ 14 , 15 ], a composite tool combining gene homologies and gene order (GRAViTy) [ 16 , 17 ], a virus domain orthologous groups approach (VDOG) [ 18 ] and a concatenated protein phylogeny of members of the order Caudovirales (CCP77) [ 19 ]. Based on this evidence, the ICTV’s Bacterial and Archaeal Viruses Subcommittee started disentangling the web of overlapping and complementary groups of tailed phages by defining new, genome-based families.…”

Long-read transcriptomics of Ostreid herpesvirus 1 uncovers a conserved expression strategy for the capsid maturation module and pinpoints a mechanism for evasion of the ADAR-based antiviral defence

“…Furthermore, it stands to reason that the amount of the protease necessary for the proteolytic processing of the scaffolding protein would be considerably lower than that of the substrate (i.e., scaffolding protein). Although it is difficult to estimate the divergence time for distantly-related viruses, the pan- Herpesvirales conservation of transcriptional architecture of the protease-scaffolding gene module has likely evolved at least in the common ancestor of vertebrate and invertebrate herpesviruses, and hence could predate the divergence of arthropods, molluscs and chordates (39,40).…”

Informative Regions In Viral Genomes

“…Besides the absence of an universal ViPhOG, a not negligible number of ViPhOGs were formed by regions from phages and eukaryotic viruses. Further analyses would be needed to determine if the fact that a ViPhOG is shared between eukaryotic and prokaryotic/archeal viruses is due to functional convergence, or if it is because those viruses presumably have an evolutionary relationship as is the case for Herpesviridae and Siphoviridae [ 42 , 43 , 44 ] or as ssRNA(+) viruses, which presumably co-evolved with their hosts before they split into eukaryotes [ 3 , 45 ].…”