Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages

Abstract Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order—Caudovirales, composed of just four families: Myoviridae, Siphoviridae,...

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Published in:Systematic biology Vol. 69; no. 1; pp. 110 - 123
Main Authors: Barylski, Jakub, Enault, François, Dutilh, Bas E, Schuller, Margo BP, Edwards, Robert A, Gillis, Annika, Klumpp, Jochen, Knezevic, Petar, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Oksanen, Hanna M, Sullivan, Matthew B, Jang, Ho Bin, Simmonds, Peter, Aiewsakun, Pakorn, Wittmann, Johannes, Tolstoy, Igor, Brister, J Rodney, Kropinski, Andrew M, Adriaenssens, Evelien M
Format: Journal Article
Language:English
Published: England Oxford University Press 01.01.2020
Subjects:
Caudovirales - classification
Caudovirales - genetics
Classification
Genome, Viral - genetics
Phylogeny
spounavirus
Caudovirales
Herelleviridae
phylogenetics
virus classification
virus taxonomy
phylogenomics
ISSN:1063-5157, 1076-836X, 1076-836X
Online Access:Get full text
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Summary:Abstract Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order—Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods—including comparative genomics, core genome analysis, and marker gene phylogenetics—to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae—a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.
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ISSN:1063-5157
1076-836X
1076-836X
DOI:10.1093/sysbio/syz036