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A Viral Tree of Life Incongruent with the Cellular Universal Tree of Life

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A Viral Tree of Life Incongruent with the Cellular Universal Tree of Life Supplementary Materials for Evolution of the PRD1-adenovirus lineage: a viral tree of life incongruent with the cellular universal tree of life Anthony C. Woo, Morgan Gaia, Julien Guglielmini, Violette Da Cunha and Patrick Forterre This pdf file includes: Fig. S1. Major capsid proteins of the PRD1-adenovirus lineage. Fig. S2. Packaging ATPases of the PRD1-adenovirus lineage. Fig. S3. Sequence similarity networks of the PRD1-adenovirus packaging ATPase proteins. Fig. S4. Maximum likelihood (ML) phylogenetic tree of the major capsid protein gene of the viruses from the PRD1-adenovirus lineage. Fig. S5. Maximum likelihood (ML) phylogenetic tree of the packaging ATPase gene of the viruses from the PRD1-adenovirus lineage. Fig. S6. Maximum likelihood (ML) phylogenetic tree of the packaging ATPase gene of the archaeoviruses and bacterioviruses from the PRD1-adenovirus lineage. Fig. S7. Maximum likelihood (ML) phylogenetic tree of the packaging ATPase gene of the double jelly-roll viruses from the PRD1-adenovirus lineage, excluding single jelly-roll viruses. Fig. S8. Maximum likelihood (ML) phylogenetic tree of the major capsid protein gene of the double jelly-roll viruses from the PRD1-adenovirus lineage, excluding the FLiP members. Fig. S9. Maximum likelihood (ML) phylogenetic tree of the concatenated major capsid protein and packaging ATPase genes, excluding the Poxviridae and the Asfarviridae. Fig. S10. Maximum likelihood phylogenetic tree of the concatenated major capsid protein and packaging ATPase genes, rooting with the DJR archaeal cluster. Fig. S11. Maximum likelihood phylogenetic tree of the concatenated major capsid protein and packaging ATPase genes, rooting with the DJR bacterial cluster II. Fig. S12. Maximum likelihood phylogenetic tree of the concatenated major capsid protein and packaging ATPase genes, rooting with the DJR cluster I. Fig. S13. Maximum likelihood phylogenetic tree of the concatenated major capsid protein and packaging ATPase genes, rooting between the DJR archaeal cluster and the DJR bacterial cluster II. Data file S1. Results of the predicted structures of the major capsid protein and the packaging ATPase genes. (separate excel file) 1 STIV Archaea Turriviridae PRD1 PM2 Bacteria Tectiviridae Corticoviridae Sputnik Polinton 1SP PBCV HEV4 Eukarya Lavidaviridae Polintoviruses NCLDV Adenoviridae Fig. S1. Major capsid proteins of the PRD1-adenovirus lineage. Major capsid proteins (MCPs) with the double jelly-roll (DJR) fold and single jelly-roll (SJR) fold (boxed in dashed lines) are arranged horizontally according to the domain of life to which their hosts are classified. Virus names are provided above the structural models of various families of bacterial, archaeal and eukaryotic viruses. The structures are coloured according to the secondary structure elements: α-helices in red; β-strands in blue; and random coil in grey. The X-ray structure of the major capsid protein of Polinton 1 SP is not available and is represented with homology-based model. Sputnik, Sputnik virophage; Polinton 1 SP, Polinton 1 Strongylocentrotus purpuratus; PBCV, Paramecium bursaria Chlorella virus; NCLDV, nucleo-cytoplasmic large DNA viruses; HAE4, Human adenovirus E4; PRD1, Enterobacteria phage PRD1; PM2, Pseudoalteromonas phage PM2; STIV, Sulfolobus turreted icosahedral virus. P23-77, Thermus virus P23-77. RCSB Protein Data Bank (PDB) accession numbers for the major capsid protein structures: Sputnik, PDB entry 3J26; PBCV, PDB entry 5TIP; HAE4, PDB entry 2BVI; PRD1, PDB entry 1HB5; PM2, PDB entry 2W0C; STIV, PDB entry 2BBD; P23-77, PDB entry 3ZMN (left) and 3ZN4 (right). 2 STIV Archaea Turriviridae PRD1 PM2 Bacteria Tectiviridae Corticoviridae Sputnik Polinton 1SP PBCV HEV4 Eukarya Lavidaviridae Polintoviruses NCLDV Adenoviridae Fig. S2. Packaging ATPases of the PRD1-adenovirus lineage. Packaging ATPases (pATPases) are arranged horizontally according to the domain of life to which their hosts are classified. Virus names are provided above the structural models of various families of bacterial, archaeal and eukaryotic viruses. The structures are coloured according to the secondary structure elements: α-helices in red; β-strands in blue; and random coil in grey. The X-ray structures of the pATPase proteins of Sputnik, Polinton 1 SP, PBCV, HAE4, PRD1, PM2 and P23-77 are not available and are represented with homology-based models. Sputnik, Sputnik virophage; Polinton 1 SP, Polinton 1 Strongylocentrotus purpuratus; PBCV, Paramecium bursaria Chlorella virus; NCLDV, nucleo-cytoplasmic large DNA viruses; HAE4, Human adenovirus E4; PRD1, Enterobacteria phage PRD1; PM2, Pseudoalteromonas phage PM2; STIV, Sulfolobus turreted icosahedral virus. P23-77, Thermus virus P23-77. RCSB Protein Data Bank (PDB) accession numbers for the pATPase structure: STIV, PDB entry 4KFU. 3 A SJR DJR Fig. S3. Sequence similarity networks of the PRD1-adenovirus packaging ATPase proteins. Protein sequences were clustered using SiLiX based on the sequence similarity. Different clusters of viruses are shown as clouds of connected colored circles, with each circle corresponding to a single pATPase protein. Members are classified according to (A) the structure of the MCP or (B) the different families/subfamilies which they belong to. Abbreviations: DJR, double jelly-roll; SJR: single jelly-roll; NCLDV, Nucleo-Cytoplasmic Large DNA Viruses; STIV, Sulfolobus turreted icosahedral virus 4 96 Cellulophaga phage phi48:2 78.7 89 Flavobacterium soli 100 Sphingobacteriaceae bacterium GW460-11-11-14-LB5 Tree scale: 1 98.9 Flavobacterium phage FLiP 98 Rhodococcus phage Toil 84.8 Streptomyces noursei ATCC 11455 100 Sulfolobus turreted icosahedral virus 1 93 100 85.9 96 Sulfolobus turreted icosahedral virus 2 82.6 100 Sulfobacillus thermosulfidooxidans MCP 100 Sulfobacillus acidophilus TPY 87 Gluconobacter phage GC1 100 Enterobacteria phage PRD1 100 100 87 99.8 91 Enterobacteria phage PR4 73.8 95 Enterobacteria phage PR3 90.8 Polintoviruses Brevibacillus sp. CF112 99 98 Bacillus pumilus 98.9 76.4 Bacillus licheniformis 98 97.5 Bacillus flexus Poxviridae 79 100 Bacillus phage Bam35c 100 94 Bacillus phage GIL16c 82 95.8 Bacillus sp. AFS075034 83.9 93 90.4 80 Bacillus phage Wip1 Bacillus virus AP50 STIV Burkholderia ubonensis 97 Pseudoalteromonas virus PM2 88.5 95 100 Kiloniella spongiae 77.5 96.5 Thioclava dalianensis 96 PM2 74.9 Autolykiviridae_1.249.A 96 99 Autolykiviridae_1.008.O 81 91.1 100 Autolykiviridae_1.020.O 99.8 91 Autolykiviridae_1.044.O Cellulomonas Autolykiviridae_1.080.O 78 Phycisphaerae bacterium SM23_30 99 Nitrospirae bacterium GWB2_47_37 96 Magnetospirillum marisnigri 100 100 73 Magnetospirillum magneticum Bam35 90 Magnetospirillum sp. ME-1 78.3 Candidatus Nitrososphaera evergladensis SR1 Archaeoglobus veneficus 97 100 94.9 100 100 Archaeal virus DEEP JUN17B 99.3 Toil 95 Archaeal virus DEEP JUN17A 91 Pyrobaculum oguniense TE7 Archaeal virus DEEP AND17J 98 Methanococcus voltae A3 99 Methanolacinia petrolearia PRD1 96.9 Methanofollis ethanolicus Thermococcus barophilus Candidatus Nitrososphaera gargensis Ga9.2 98 Thermococcus kodakarensis 72 91 Phycodnaviridae 98 Palaeococcus ferrophilus 88.7 Thermococcus guaymasensis 95 79.8 100 Thermococcus nautili 95.3 pTN3 Mimiviridae Polinton_1_DY 100 Polinton_2_NV 91 Polinton_1_TC 89 100 Polinton_2_DR 70.6 100 89 Polinton_1_DR 73 Mimiviridae-related 100 Polinton_1_SP 100 Polinton_2_SP Yellowstone Lake virophage 7 96 92.9 Cafeteriavirus-dependent mavirus Organic Lake virophage Mollivirus 100 96.1 Yellowstone Lake virophage 6 100 98.4 Qinghai Lake virophage 89 Dishui lake virophage 1 88 Yellowstone Lake virophage 5 Iridoviridae II 71.9 94 100 Sputnik virophage 100 Zamilon virus 86 85 Melanoplus sanguinipes entomopoxvirus 100 Anomala cuprea entomopoxvirus 100 Iridoviridae I 99 Choristoneura biennis entomopoxvirus 100 90.8 Amsacta moorei entomopoxvirus 100 Myxoma virus 100 Variola virus 99.9 96 Ascoviridae 79.8 99 Canarypox virus 88.9 Bovine papular stomatitis virus African swine fever virus 85 100 83.2 99.6 100 Kaumoebavirus 91.4 Faustovirus Marseilleviridae 100 Trichoplusia ni ascovirus 2c 98.7 Spodoptera frugiperda ascovirus 1a 97 95.5 Frog virus 3 100 Red seabream iridovirus 99.3 97 Lymphocystis disease virus 1 Asfarviridae 75.7 82 100 Invertebrate iridescent virus 6 91.2 96 Invertebrate iridovirus 25 85.9 Lausannevirus 100 100 100 Marseillevirus marseillevirus Lavidaviridae 87 73.3 82.1 Melbournevirus 100 Acanthocystis turfacea Chlorella virus Can0610SP 96.4 Paramecium bursaria Chlorella virus NE-JV-1 98 84.9 99 Yellowstone lake phycodnavirus 2 93 FLiP 100 Yellowstone lake phycodnavirus 3 100 Ostreococcus tauri virus OtV5 99 95.2 99 Micromonas pusilla virus 12T 99 94 99.6 Bathycoccus sp. RCC1105 virus BpV2 Heterosigma akashiwo virus 01 100 Emiliania huxleyi virus 202 97.3 Mollivirus sibericum 88 92.9 100 Organic Lake phycodnavirus 1 99.7 Phaeocystis globosa virus 94 85.9 Acanthamoeba polyphaga moumouvirus 96 100 Hokovirus HKV1 90.9 96.8 96 Klosneuvirus KNV1 100 Acanthamoeba polyphaga mimivirus 100 Acanthamoeba castellanii mamavirus Fig. S4. Maximum likelihood (ML) phylogenetic tree of the major capsid protein gene of the viruses from the PRD1-adenovirus lineage. The root of the ML phylogenetic tree was between the prokaryotic and eukaryotic members. The scale-bar indicates the average number of substitutions per site. Values on top and below branches represent support calculated by ultrafast bootstrap approximation (UFBoot; 1,000 replicates) and SH-like approximate likelihood ratio test (aLRT; 1,000 replicates),
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