DOI: 10.5061/dryad.106q6g6
title: Data from: Analysis of spounaviruses as a case study for the overdue reclassification of tailed phages

description: 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
 towards much-needed re-classification in the Caudovirales order.
description: Figure
 S1Virus Proteomic Tree of
 all dsDNA viruses in the Virus-Host DB as computed by VIPTree (May
 2018)Figure
 S2Matrices and heat-maps
 representing distance and similarity scores generated using different
 comparison tools (Gegenees, DICE and GET_HOMOLOGUES).Figure
 S3Maximum Likelihood
 single marker gene phylogenetic trees. Multiple alignments of amino acid
 sequences were made with Clustal Omega and trees were built with IQTree.
 The scale bar represents the number of substitutions per site. Branches
 corresponding to genera and suggested subfamilies are delineated with
 colored squares and circles, respectively.Supplementary File 1
 Materials & MethodsDetailed description of
 the materials and methods used in this manuscript.Table
 S1Overview of the all
 phage genomes used in this study.Table
 S2Complete list of all
 protein clusters identified in the set of 93 herellevirus
 genomes.Table
 S3Topological distances
 (Robinson–Foulds distances) between different trees presented in this
 paper. Al distances were calculated using IQTree suite.Figure
 S4Tanglegram comparisons
 of the topologies of the dendrograms generated by the different analysis
 tools.Supplement to Figure 1b
 GRAViTy dendrogramNewick file of the
 dendrogram in Figure 1b as generated with GRAViTy.1.b.GRAViTy_BootstrappedUPGMATree.nwkSupplement to Figure 2a VICTOR treeNewick file of the tree in Figure 2a generated by VICTOR.2.a.VICTOR.nucl_genomes.nwkSupplement to Figure 2b DICE treeNewick file of the tree in Figure 2b, DICE scores.2.b.DICE.transl_genomes.nwkSupplement to Figure 3a VIPTreeNewick file of the tree in Figure 3a as generated by the VIPtree server (Nishimura et al, 2017).3.a.VipTree.proteome.nwkSupplement to Figure 3b GOAT treeNewick file of the tree in Figure 3b as generated by GOAT.3.b.GOAT.synteny.nwkSupplement to Figure 4 concatenated marker treeNewick file of the tree in Figure 4 generated by IQtree on the multiple alignment of 10 marker genes.4.IQtree.concatenated_markers_10.nwk