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

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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).

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.

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), respectively. Only values superior to 70 are shown. The best-fit model was LG + F + R4, which was chosen according to Bayesian Information Criterion (BIC). The alignment has 107 sequences with 262 positions.

SJR 1714273 NP 777329 Thermus virus IN93 100 SJR 884155 WP 119341505 Meiothermus hypogaeus Tree scale: 1 99.8 84 72.8 82 SJR 1714272 YP 003169720 Thermus virus P23-77 SJR 1930763 WP 114314098 Thermus caldifontis 100 Kiloniella spongiae 99.9 Thioclava dalianensis 99 96 Autolykiviridae_1.249.A 100 Autolykiviridae_1.008.O pATPase 100 100 Autolykiviridae_1.080.O 96.4 98 100 Autolykiviridae_1.020.O 75.4 Autolykiviridae_1.044.O 100 Archaeal virus DEEP AND17J 86 99.8 Methanococcus voltae A3 Polintoviruses 85.7 97 Pseudoalteromonas virus PM2 88.2 Burkholderia ubonensis SJR 57705 WP 126967128 Halomicrobium mukohataei 75.3 100 99.2 SJR fig 1723446.5.peg.25 Gene23 Natrinema virus SNJ1 76 100 76 95.9 100 SJR 353800 WP 049952269 Halostagnicola larsenii Poxviridae 94 83.3 89.4 SJR 51589 WP 129755687 Haloarcula hispanica SJR 453847 WP 049970559 Haladaptatus cibarius 99 SJR 1154689 YP 005352793 Haloarcula hispanica icosahedral virus 2 99.1 94 SJR 1735722 YP 009272833 Haloarcula californiae icosahedral virus 1 84.7 92 99 SJR 326574 YP 271874 Haloarcula hispanica virus SH1 STIV 91.4 SJR 1282967 YP 007761602 Haloarcula hispanica virus PH1 98 Streptomyces noursei ATCC 11455 90 80 Rhodococcus phage Toil Gluconobacter phage GC1 70 100 Enterobacteria phage PR4 87.4 100 100 PM2 97.9 100 Enterobacteria phage PR3 93 94.4 Enterobacteria phage PRD1 100 Sulfobacillus acidophilus TPY 100 Sulfobacillus thermosulfidooxidans 98 89.5 Brevibacillus sp. CF112 Cellulomonas 100 Bacillus flexus 95.7 99 99 Bacillus phage GIL16c 92.7 97.4 Bacillus phage Bam35c 92 84.6 100 Bacillus licheniformis 99.8 93 Bacillus pumilus 84.2 Bacillus sp. AFS075034 Bam35 100 99.8 97 Bacillus phage Wip1 72.6 Bacillus virus AP50 Candidatus Nitrososphaera gargensis Ga9.2 88.4 Candidatus Nitrososphaera evergladensis SR1 Pyrobaculum oguniense TE7 Toil 74 89.3 80.6 89.3 100 Sulfolobus turreted icosahedral virus 2 99.9 Sulfolobus turreted icosahedral virus 1 78.1 Phycisphaerae bacterium SM23_30 94 Nitrospirae bacterium GWB2_47_37 96 86 Magnetospirillum sp. ME-1 PRD1 100 100 78 Magnetospirillum marisnigri Magnetospirillum magneticum Archaeoglobus veneficus 99 89.9100 Archaeal virus DEEP JUN17B 96.6 Archaeal virus DEEP JUN17A Phycodnaviridae 100 100 100 Methanofollis ethanolicus 96.2 Methanolacinia petrolearia 93 73.9 Thermococcus barophilus 100 100 Thermococcus kodakarensis 100 93 Mimiviridae 99 Palaeococcus ferrophilus 89.3 Thermococcus guaymasensis 99 71.6 100 pTN3 88.3 Thermococcus nautili Cafeteriavirus-dependent mavirus 99 Yellowstone Lake virophage 7 Mimiviridae-related 95 100 Organic Lake virophage 94.1 Yellowstone Lake virophage 5 93.4 73 93.4 80.9 100 Sputnik virophage 73 99.6 Zamilon virus 90.4 Yellowstone Lake virophage 6 Mollivirus 72 99 Dishui lake virophage 1 90.6 Qinghai Lake virophage 100 Polinton_2_DR 93.3 Polinton_1_DR 100 Iridoviridae II 100 100 Polinton_1_SP 100 88 Polinton_2_SP Polinton_2_NV 91 99 Polinton_1_DY 91 88 Polinton_1_TC 78.9 Iridoviridae I 79 Melanoplus sanguinipes entomopoxvirus 100 Anomala cuprea entomopoxvirus 99.8 98 Choristoneura biennis entomopoxvirus 99 75.1 Amsacta moorei entomopoxvirus 87.5 Variola virus 100 99.3 Myxoma virus Ascoviridae 92 95 83.2 84.8 98 Canarypox virus 81.6 Bovine papular stomatitis virus African swine fever virus 100 99.2 Kaumoebavirus Marseilleviridae Faustovirus Marseillevirus marseillevirus 100 92 99.8 91 Melbournevirus Lausannevirus Invertebrate iridescent virus 6 93 89.2 100 Trichoplusia ni ascovirus 2c Asfarviridae 100 100 98 Spodoptera frugiperda ascovirus 1a 92.5 99.1 Invertebrate iridovirus 25 70 Frog virus 3 100 99.9 96 Red seabream iridovirus Lavidaviridae Lymphocystis disease virus 1 82 100 Phaeocystis globosa virus 86.6 96.8 96 Organic Lake phycodnavirus 1 90.6 Klosneuvirus KNV1 99 Hokovirus HKV1 93.3 99 Acanthamoeba polyphaga moumouvirus 100 Gamma-Sphaerolipovirus 100 Acanthamoeba polyphaga mimivirus 84 100 94.6 96.3 Acanthamoeba castellanii mamavirus 82 Emiliania huxleyi virus 202 96.4 Mollivirus sibericum 80 100 Acanthocystis turfacea Chlorella virus Can0610SP 87.7 Beta-Sphaerolipovirus 100 Paramecium bursaria Chlorella virus NE-JV-1 79 Heterosigma akashiwo virus 01 97 Yellowstone lake phycodnavirus 3 99.5 84 Yellowstone lake phycodnavirus 2 71.1 Bathycoccus sp. RCC1105 virus BpV2 84 Alpha-Sphaerolipovirus 88 Ostreococcus tauri virus OtV5 80.3 Micromonas pusilla virus 12T Fig. S5. Maximum likelihood (ML) phylogenetic tree of the packaging ATPase 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), respectively. Only values superior to 70 are shown. The best-fit model was LG + R6, which was chosen according to Bayesian Information Criterion (BIC). The alignment has 116 sequences with 151 positions.

6 Tree scale: 0.1 88 Streptomyces noursei ATCC 11455 66.8 Rhodococcus phage Toil 79 76.8 Gluconobacter phage GC1 100 Enterobacteria phage PR4 pATPase 100 100 97.6 Enterobacteria phage PR3 94 100 91.3 Enterobacteria phage PRD1 STIV 100 Sulfobacillus acidophilus TPY 100 Sulfobacillus thermosulfidooxidans 98 93.2 Brevibacillus sp. CF112 PM2 100 Bacillus flexus 97.2 99 100 Bacillus phage GIL16c Cellulomonas 96.8 99.9 Bacillus phage Bam35c 100 Bacillus licheniformis 99.7 Bacillus pumilus 78 Bacillus virus AP50 Bam35 100 99.6 75 Bacillus phage Wip1 Bacillus sp. AFS075034 Toil Pyrobaculum oguniense TE7 83.2 100 Sulfolobus turreted icosahedral virus 2 99.9 Sulfolobus turreted icosahedral virus 1 PRD1 Phycisphaerae bacterium SM23_30 86.7 93 96.5 100 Kiloniella spongiae 92 99.9 Thioclava dalianensis Gamma-Sphaerolipovirus 92.4 Nitrospirae bacterium GWB2_47_37 95 Magnetospirillum marisnigri 80.6 100 Beta-Sphaerolipovirus 99.9 97 Magnetospirillum magneticum Magnetospirillum sp. ME-1 84 Candidatus Nitrososphaera gargensis Ga9.2 Alpha-Sphaerolipovirus 91.5 Candidatus Nitrososphaera evergladensis SR1 100 Archaeal virus DEEP AND17J 100 Methanococcus voltae A3 83.7 93 Pseudoalteromonas virus PM2 88.2 Burkholderia ubonensis Autolykiviridae_1.249.A 100 100 Autolykiviridae_1.008.O 100 Autolykiviridae_1.080.O 97.1 99 99 Autolykiviridae_1.020.O 73.7 Autolykiviridae_1.044.O SJR 1930763 WP 114314098 Thermus caldifontis 100 100 SJR 1714273 NP 777329 Thermus virus IN93 SJR 1714272 YP 003169720 Thermus virus P23-77 SJR 884155 WP 119341505 Meiothermus hypogaeus SJR 57705 WP 126967128 Halomicrobium mukohataei 100 SJR fig 1723446.5.peg.25 Gene23 Natrinema virus SNJ1 99.6 100 93.5 SJR 353800 WP 049952269 Halostagnicola larsenii 91.3 97 96 76 95.2 SJR 51589 WP 129755687 Haloarcula hispanica SJR 453847 WP 049970559 Haladaptatus cibarius 100 99.9 SJR 1154689 YP 005352793 Haloarcula hispanica icosahedral virus 2 91 SJR 1735722 YP 009272833 Haloarcula californiae icosahedral virus 1 72.5 92 76.1 92 SJR 326574 YP 271874 Haloarcula hispanica virus SH1 92.7 SJR 1282967 YP 007761602 Haloarcula hispanica virus PH1 Archaeoglobus veneficus 98 91.2 100 Archaeal virus DEEP JUN17B 98.6 Archaeal virus DEEP JUN17A 100 99.8 99 Methanofollis ethanolicus 93.6 Methanolacinia petrolearia 98 92.1 Thermococcus barophilus 100 99 Thermococcus kodakarensis 100 92.2 Palaeococcus ferrophilus 98 90.7 Thermococcus guaymasensis 94 99 pTN3 94 Thermococcus nautili Fig. S6. Maximum likelihood (ML) phylogenetic tree of the packaging ATPase gene of the archaeoviruses and bacterioviruses from the PRD1-adenovirus lineage. The ML phylogenetic tree was rooted with the members of the Tectiviridae, which includes the PRD1, the Bam35 and the Toil. 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), respectively. Only values superior to 70 are shown. The best-fit model was LG + R4, which was chosen according to Bayesian Information Criterion (BIC). The alignment has 62 sequences with 185 positions.

7 Autolykiviridae_1.249.A 100 Autolykiviridae_1.008.O 100 99 Autolykiviridae_1.080.O Tree scale: 1 93.4 99 71.9 99 Autolykiviridae_1.020.O 75 Autolykiviridae_1.044.O Pyrobaculum oguniense TE7 94 85.5 100 Sulfolobus turreted icosahedral virus 2 100 Sulfolobus turreted icosahedral virus 1 Archaeoglobus veneficus 97 94 100 Archaeal virus DEEP JUN17B 99 98.5 Archaeal virus DEEP JUN17A 92 100 100 99 Methanofollis ethanolicus 94.1 Methanolacinia petrolearia 84 Thermococcus barophilus 100 100 Thermococcus kodakarensis 100 93.1 100 Palaeococcus ferrophilus 92.6 Thermococcus guaymasensis 99 93.2 99 pTN3 96.6 Thermococcus nautili 95 Candidatus Nitrososphaera gargensis Ga9.2 94.7 Candidatus Nitrososphaera evergladensis SR1 Burkholderia ubonensis 91 86 Pseudoalteromonas virus PM2 79.3 87 72 100 Archaeal virus DEEP AND17J 99.8 Methanococcus voltae A3 Phycisphaerae bacterium SM23_30 91 77.5 100 Kiloniella spongiae 88 99.7 Thioclava dalianensis 70.6 Nitrospirae bacterium GWB2_47_37 Magnetospirillum marisnigri 100 100 100 Magnetospirillum magneticum 72.6 Magnetospirillum sp. ME-1 90 Streptomyces noursei ATCC 11455 Rhodococcus phage Toil 81 Gluconobacter phage GC1 100 Enterobacteria phage PR4 99.9 100 98.5 Enterobacteria phage PR3 90 100 89.8 Enterobacteria phage PRD1 Sulfobacillus acidophilus TPY 100 Sulfobacillus thermosulfidooxidans 98 88.9 Brevibacillus sp. CF112 100 Bacillus flexus 96.3 100 100 Bacillus phage GIL16c 94.1 99.2 Bacillus phage Bam35c 82 75.6 100 Bacillus licheniformis 99.9 83 Bacillus pumilus Bacillus sp. AFS075034 100 99.5 99 Bacillus phage Wip1 89.2 Bacillus virus AP50 Cafeteriavirus-dependent mavirus 100 Yellowstone Lake virophage 5 99.2 Organic Lake virophage 99 90 90.2 82.3 90 Yellowstone Lake virophage 7 97 82.1 Yellowstone Lake virophage 6 95 Qinghai Lake virophage 96 Dishui lake virophage 1 86.9 96 100 Sputnik virophage 100 Zamilon virus Polinton_2_NV 100 100 Polinton_1_SP 100 99.8 Polinton_2_SP 89 Polinton_1_DY Polinton_1_TC Polinton_2_DR 93 100 76.1 99.3 Polinton_1_DR Melanoplus sanguinipes entomopoxvirus 100 Anomala cuprea entomopoxvirus 99.2 99 81 99 Choristoneura biennis entomopoxvirus 99 81.7 93 Amsacta moorei entomopoxvirus Canarypox virus 100 Bovine papular stomatitis virus 99.5 99 88.6 98 Variola virus Myxoma virus Kaumoebavirus 99 93 98 African swine fever virus 70.1 Faustovirus Lausannevirus 100 96 99.4 95 Marseillevirus marseillevirus 81.1 Melbournevirus Frog virus 3 100 99.9 100 Red seabream iridovirus 88.2 98.3 96 Lymphocystis disease virus 1 85.1 98.3 Invertebrate iridovirus 25 90 Invertebrate iridescent virus 6 95 83.4 100 Trichoplusia ni ascovirus 2c 100 Spodoptera frugiperda ascovirus 1a 89 100 Phaeocystis globosa virus 87.7 98.1 Organic Lake phycodnavirus 1 75 93.4 Klosneuvirus KNV1 98 Hokovirus HKV1 95.3 98 Acanthamoeba polyphaga moumouvirus 100 92 99.9 100 Acanthamoeba polyphaga mimivirus 96.5 99.1 Acanthamoeba castellanii mamavirus 98 Emiliania huxleyi virus 202 98.6 Mollivirus sibericum 73 Acanthocystis turfacea Chlorella virus Can0610SP 82.7 100 100 Paramecium bursaria Chlorella virus NE-JV-1 72 Heterosigma akashiwo virus 01 99 Yellowstone lake phycodnavirus 3 99.8 93 Yellowstone lake phycodnavirus 2 90.4 Bathycoccus sp. RCC1105 virus BpV2 85 95 Ostreococcus tauri virus OtV5 85.3 Micromonas pusilla virus 12T 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. 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), respectively. Only values superior to 70 are shown. The best-fit model was LG + F+ R6, which was chosen according to Bayesian Information Criterion (BIC). The alignment has 103 sequences with 171 positions.

8 100 Rhodococcus phage Toil Tree scale: 1 98.1 Streptomyces noursei ATCC 11455 100 Sulfobacillus thermosulfidooxidans 100 Sulfobacillus acidophilus TPY Gluconobacter phage GC1 100 Enterobacteria phage PRD1 99 100 100 Enterobacteria phage PR4 94 Enterobacteria phage PR3 85.9 Brevibacillus sp. CF112 Bacillus flexus 100 95 MCP 99.9 89.2 99 Bacillus pumilus 98.6 Bacillus licheniformis 99 94.4 100 Bacillus phage Bam35c 100 97 Bacillus phage GIL16c 77.5 Bacillus virus AP50 Polintoviruses 100 91 99.7 Bacillus sp. AFS075034 94.5 74 Bacillus phage Wip1 99 Phycisphaerae bacterium SM23_30 93.9 Poxviridae 98 Nitrospirae bacterium GWB2_47_37 97.1 Magnetospirillum marisnigri 100 100 99 Magnetospirillum magneticum 78.9 Magnetospirillum sp. ME-1 Burkholderia ubonensis STIV Pseudoalteromonas virus PM2 99 94 97.1 100 Kiloniella spongiae 97.6 98 Thioclava dalianensis 88.2 Autolykiviridae_1.249.A PM2 78 98 99 Autolykiviridae_1.008.O 92.4 95.9 87.2 100 Autolykiviridae_1.020.O 99.5 100 Autolykiviridae_1.044.O 93.4 Autolykiviridae_1.080.O Candidatus Nitrososphaera gargensis Ga9.2 Cellulomonas 90 93.6 100 Sulfolobus turreted icosahedral virus 1 100 Sulfolobus turreted icosahedral virus 2 84.2 Candidatus Nitrososphaera evergladensis SR1 Archaeoglobus veneficus Bam35 78 100 100 99 Archaeal virus DEEP JUN17B 99 95 Archaeal virus DEEP JUN17A 79.1 Pyrobaculum oguniense TE7 100 Methanococcus voltae A3 Toil 99.2 70 97 Methanolacinia petrolearia 96 Methanofollis ethanolicus 71.4 Archaeal virus DEEP AND17J Thermococcus barophilus PRD1 98 97 Thermococcus kodakarensis 97.2 84 Palaeococcus ferrophilus 100 Thermococcus guaymasensis 99 Thermococcus nautili Phycodnaviridae 95.9 pTN3 Polinton_2_NV 100 100 Polinton_1_DY 98 Polinton_1_TC 93.9 98 100 Polinton_2_DR Mimiviridae 90.4 100 98 Polinton_1_DR 90.5 100 Polinton_1_SP 100 Polinton_2_SP African swine fever virus Mimiviridae-related 99.7 99.7 98 Kaumoebavirus 74.5 Faustovirus Cafeteriavirus-dependent mavirus 99 Yellowstone Lake virophage 7 96.4 Mollivirus 99 Organic Lake virophage 94.2 79 99 Yellowstone Lake virophage 6 Qinghai Lake virophage 99 95 Dishui lake virophage 1 96 Iridoviridae II Yellowstone Lake virophage 5 99 90.7 100 Sputnik virophage 100 Zamilon virus 100 Acanthocystis turfacea Chlorella virus Can0610SP Iridoviridae I 88 97.8 Paramecium bursaria Chlorella virus NE-JV-1 90 85 88.8 Bathycoccus sp. RCC1105 virus BpV2 100 100 Micromonas pusilla virus 12T 70 82 Ostreococcus tauri virus OtV5 72 70 Ascoviridae 82.4 95.2 100 Yellowstone lake phycodnavirus 2 100 Yellowstone lake phycodnavirus 3 Emiliania huxleyi virus 202 79 Heterosigma akashiwo virus 01 76.2 Marseilleviridae 91 100 Organic Lake phycodnavirus 1 99.9 Phaeocystis globosa virus 93 84.4 Acanthamoeba polyphaga moumouvirus 99 100 Hokovirus HKV1 92.2 97.6 99 Klosneuvirus KNV1 Asfarviridae 86.3 100 Acanthamoeba polyphaga mimivirus 100 Acanthamoeba castellanii mamavirus Mollivirus sibericum Anomala cuprea entomopoxvirus 100 Lavidaviridae Melanoplus sanguinipes entomopoxvirus 99.8 96 100 Choristoneura biennis entomopoxvirus 100 100 73.5 99.9 Amsacta moorei entomopoxvirus Bovine papular stomatitis virus 100 Canarypox virus 99.9 93 73.9 95 Variola virus 71.1 85.9 Myxoma virus 100 Trichoplusia ni ascovirus 2c 99.2 Spodoptera frugiperda ascovirus 1a 100 Red seabream iridovirus 95.6 95 Lymphocystis disease virus 1 100 Frog virus 3 75 100 Invertebrate iridescent virus 6 73 99.8 79 Invertebrate iridovirus 25 80.8 Lausannevirus 100 100 97 Marseillevirus marseillevirus Melbournevirus 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. 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), respectively. Only values superior to 70 are shown. The best-fit model was LG + F + R4, which was chosen according to Bayesian Information Criterion (BIC). The alignment has 103 sequences with 237 positions.

9 Rhodococcus phage Toil Tree scale: 1 0.97 Streptomyces noursei ATCC 11455 0.78 Gluconobacter phage GC1 1.00 Enterobacteria phage PRD1 1.00 Enterobacteria phage PR4 0.47 0.92 Enterobacteria phage PR3 Sulfobacillus thermosulfidooxidans 1.00 Sulfobacillus acidophilus TPY Brevibacillus sp. CF112 0.97 Bacillus phage Bam35c 1.00 1.00 Bacillus phage GIL16c cluster II Bacillus virus AP50

1.00 DJR bacterial 1.00 Bacillus sp. AFS075034 0.51 Bacillus phage Wip1 0.84 Bacillus flexus 0.93 Bacillus pumilus 1.00 Bacillus licheniformis 1.00 Phycisphaerae bacterium SM23_30 0.77 Nitrospirae bacterium GWB2_47_37 1.00 Magnetospirillum marisnigri 1.00 Magnetospirillum magneticum 0.79 Magnetospirillum sp. ME-1 0.87 Pseudoalteromonas virus PM2 0.77 Burkholderia ubonensis Kiloniella spongiae 0.97 1.00 Thioclava dalianensis cluster I 0.91 Autolykiviridae_1.249.A

Autolykiviridae_1.008.O DJR bacterial 0.70 1.00 0.81 Autolykiviridae_1.020.O 1.00 Autolykiviridae_1.044.O 0.94 Autolykiviridae_1.080.O Sulfolobus turreted icosahedral virus 1 1.00 Sulfolobus turreted icosahedral virus 2 Candidatus Nitrososphaera evergladensis SR1 0.96 0.76 Candidatus Nitrososphaera gargensis Ga9.2 Pyrobaculum oguniense TE7 0.95 Archaeal virus DEEP AND17J 0.99 1.00 Methanococcus voltae A3 Archaeoglobus veneficus 0.96 1.00 Archaeal virus DEEP JUN17B 1.00 Archaeal virus DEEP JUN17A 0.92 Methanolacinia petrolearia 0.99 Methanofollis ethanolicus cluster 0.90 Thermococcus barophilus

Red seabream iridovirus eukaryoviruses 0.98 Lymphocystis disease virus 1 0.52 1.00 Frog virus 3 Acanthocystis turfacea Chlorella virus Can0610SP 0.99 Paramecium bursaria Chlorella virus NE-JV-1 0.87 Yellowstone lake phycodnavirus 2 1.00 Yellowstone lake phycodnavirus 3 1.00 Ostreococcus tauri virus OtV5 0.94 Micromonas pusilla virus 12T 0.83 0.78 Bathycoccus sp. RCC1105 virus BpV2 Emiliania huxleyi virus 202 0.49 Mollivirus sibericum 0.88 Heterosigma akashiwo virus 01 Organic Lake phycodnavirus 1 0.91 1.00 Phaeocystis globosa virus 1.00 Hokovirus HKV1 0.98 Klosneuvirus KNV1 1.00 Acanthamoeba polyphaga moumouvirus 1.00 Acanthamoeba polyphaga mimivirus 1.00 Acanthamoeba castellanii mamavirus Fig. S9. Maximum likelihood (ML) phylogenetic tree of the concatenated major capsid protein and packaging ATPase genes, excluding the Poxviridae and the Asfarviridae. The ML phylogenetic tree was rooted between the prokaryotic and eukaryotic members. The scale-bar indicates the average number of substitutions per site. Values on the branches represent transfer bootstrap expectation (TBE) support calculated by nonparametric bootstrap (1,000 replicates). The best-fit model was LG + F + R4, which was chosen according to Bayesian Information Criterion (BIC). The alignment has 92 sequences with 425 positions.

10 Sulfolobus turreted icosahedral virus 1 1.00 Sulfolobus turreted icosahedral virus 2 Candidatus Nitrososphaera evergladensis SR1 Tree scale: 1 0.96 0.76 Candidatus Nitrososphaera gargensis Ga9.2 Pyrobaculum oguniense TE7 0.95 Archaeal virus DEEP AND17J 0.99 1.00 Methanococcus voltae A3 Concatenated Archaeoglobus veneficus 0.96 1.00 Archaeal virus DEEP JUN17B 1.00 Archaeal virus DEEP JUN17A 0.92 Methanolacinia petrolearia

Polintoviruses 0.99 Methanofollis ethanolicus cluster 0.90 Thermococcus barophilus

Thermococcus kodakarensis DJR archaeal 1.00 STIV 0.79 Palaeococcus ferrophilus 1.00 Thermococcus guaymasensis 0.88 Thermococcus nautili 1.00 pTN3 PM2 Phycisphaerae bacterium SM23_30 0.77 Nitrospirae bacterium GWB2_47_37 1.00 Magnetospirillum marisnigri 1.00 Magnetospirillum magneticum Cellulomonas 0.79 Magnetospirillum sp. ME-1 0.87 Pseudoalteromonas virus PM2 0.77 Burkholderia ubonensis Kiloniella spongiae Bam35 0.97 1.00 Thioclava dalianensis cluster I 0.91 Autolykiviridae_1.249.A Autolykiviridae_1.008.O 1.00 DJR bacterial Toil 0.81 Autolykiviridae_1.020.O 1.00 Autolykiviridae_1.044.O 0.94 Autolykiviridae_1.080.O PRD1 Rhodococcus phage Toil 0.97 Streptomyces noursei ATCC 11455 0.78 Gluconobacter phage GC1 1.00 Enterobacteria phage PRD1 Phycodnaviridae 1.00 Enterobacteria phage PR4 0.47 0.92 Enterobacteria phage PR3 Sulfobacillus thermosulfidooxidans Mimiviridae 1.00 Sulfobacillus acidophilus TPY Brevibacillus sp. CF112 0.97 Bacillus phage Bam35c 1.00 1.00 Bacillus phage GIL16c

Mimiviridae-related Bacillus virus AP50 cluster II 1.00 1.00 Bacillus sp. AFS075034 DJR bacterial 0.51 Bacillus phage Wip1 0.84 Bacillus flexus Mollivirus 0.93 Bacillus pumilus 0.70 1.00 Bacillus licheniformis Cafeteriavirus-dependent mavirus Iridoviridae II 1.00 Yellowstone Lake virophage 7 0.98 Organic Lake virophage 0.99 Yellowstone Lake virophage 6 Iridoviridae I 0.92 Qinghai Lake virophage 0.76 Dishui lake virophage 1 0.63 Yellowstone Lake virophage 5 0.80 Sputnik virophage Ascoviridae 1.00 Zamilon virus Polinton_2_NV 1.00 1.00 Polinton_1_DY Polinton_1_TC 0.94 Marseilleviridae Polinton_2_DR 0.90 1.00 Polinton_1_DR 0.86 Polinton_1_SP Lavidaviridae 1.00 Polinton_2_SP Trichoplusia ni ascovirus 2c 1.00 Spodoptera frugiperda ascovirus 1a 0.94 Invertebrate iridescent virus 6 0.99 0.97 Invertebrate iridovirus 25 Lausannevirus

0.92 DJR 1.00 Marseillevirus marseillevirus 0.92 Melbournevirus 0.73 Red seabream iridovirus

0.98 Lymphocystis disease virus 1 eukaryoviruses 0.52 1.00 Frog virus 3 Acanthocystis turfacea Chlorella virus Can0610SP 0.99 Paramecium bursaria Chlorella virus NE-JV-1 0.87 Yellowstone lake phycodnavirus 2 1.00 Yellowstone lake phycodnavirus 3 1.00 Ostreococcus tauri virus OtV5 0.94 Micromonas pusilla virus 12T 0.83 0.78 Bathycoccus sp. RCC1105 virus BpV2 Emiliania huxleyi virus 202 0.49 Mollivirus sibericum 0.88 Heterosigma akashiwo virus 01 Organic Lake phycodnavirus 1 0.91 1.00 Phaeocystis globosa virus 1.00 Hokovirus HKV1 0.98 Klosneuvirus KNV1 1.00 Acanthamoeba polyphaga moumouvirus 1.00 Acanthamoeba polyphaga mimivirus 1.00 Acanthamoeba castellanii mamavirus Fig. S10. Maximum likelihood phylogenetic tree of the concatenated major capsid protein and packaging ATPase genes, rooting with the DJR archaeal cluster. The scale- bar indicates the average number of substitutions per site. Values on the branches represent transfer bootstrap expectation (TBE) support calculated by nonparametric bootstrap (1,000 replicates). The best-fit model was LG + F + R4, which was chosen according to Bayesian Information Criterion (BIC). The alignment has 92 sequences with 425 positions.

11 Rhodococcus phage Toil 0.97 Streptomyces noursei ATCC 11455 Tree scale: 1 0.78 Gluconobacter phage GC1 1.00 Enterobacteria phage PRD1 1.00 Enterobacteria phage PR4 0.47 0.92 Enterobacteria phage PR3 Sulfobacillus thermosulfidooxidans 1.00 Sulfobacillus acidophilus TPY Brevibacillus sp. CF112 0.97 Bacillus phage Bam35c 1.00 1.00 Bacillus phage GIL16c cluster II Bacillus virus AP50 1.00 1.00 Bacillus sp. AFS075034 DJR bacterial 0.51 Bacillus phage Wip1 0.84 Bacillus flexus 0.93 Bacillus pumilus 1.00 Bacillus licheniformis Phycisphaerae bacterium SM23_30 0.77 Nitrospirae bacterium GWB2_47_37 1.00 Magnetospirillum marisnigri 1.00 Magnetospirillum magneticum 0.79 Magnetospirillum sp. ME-1 0.87 Pseudoalteromonas virus PM2 0.77 Burkholderia ubonensis Kiloniella spongiae 0.97 1.00

Thioclava dalianensis cluster I 0.91 Autolykiviridae_1.249.A

Autolykiviridae_1.008.O DJR bacterial 0.70 1.00 0.81 Autolykiviridae_1.020.O 1.00 Autolykiviridae_1.044.O 0.94 Autolykiviridae_1.080.O Sulfolobus turreted icosahedral virus 1 1.00 Sulfolobus turreted icosahedral virus 2 Candidatus Nitrososphaera evergladensis SR1 0.96 0.76 Candidatus Nitrososphaera gargensis Ga9.2 Pyrobaculum oguniense TE7 0.95 Archaeal virus DEEP AND17J 0.99 1.00 Methanococcus voltae A3 Archaeoglobus veneficus 0.96 1.00 Archaeal virus DEEP JUN17B 1.00 Archaeal virus DEEP JUN17A 0.92 Methanolacinia petrolearia cluster 0.99 Methanofollis ethanolicus 0.90 Thermococcus barophilus

Thermococcus kodakarensis DJR archaeal 1.00 0.79 Palaeococcus ferrophilus 1.00 Thermococcus guaymasensis 0.88 Thermococcus nautili 1.00 pTN3 Cafeteriavirus-dependent mavirus 1.00 Yellowstone Lake virophage 7 0.98 Organic Lake virophage 0.99 Yellowstone Lake virophage 6 0.92 Qinghai Lake virophage 0.76 Dishui lake virophage 1 0.63 Yellowstone Lake virophage 5 0.80 Sputnik virophage 1.00 Zamilon virus Polinton_2_NV 1.00 1.00 Polinton_1_DY Polinton_1_TC 0.94 Polinton_2_DR 0.90 1.00 Polinton_1_DR 0.86 Polinton_1_SP 1.00 Polinton_2_SP Trichoplusia ni ascovirus 2c 1.00 Spodoptera frugiperda ascovirus 1a 0.94 Invertebrate iridescent virus 6 0.99 0.97 Invertebrate iridovirus 25 DJR Lausannevirus 0.92 1.00 Marseillevirus marseillevirus 0.92 Melbournevirus 0.73 Red seabream iridovirus eukaryoviruses 0.98 Lymphocystis disease virus 1 0.52 1.00 Frog virus 3 Acanthocystis turfacea Chlorella virus Can0610SP 0.99 Paramecium bursaria Chlorella virus NE-JV-1 0.87 Yellowstone lake phycodnavirus 2 1.00 Yellowstone lake phycodnavirus 3 1.00 Ostreococcus tauri virus OtV5 0.94 Micromonas pusilla virus 12T 0.83 0.78 Bathycoccus sp. RCC1105 virus BpV2 Emiliania huxleyi virus 202 0.49 Mollivirus sibericum 0.88 Heterosigma akashiwo virus 01 Organic Lake phycodnavirus 1 0.91 1.00 Phaeocystis globosa virus 1.00 Hokovirus HKV1 0.98 Klosneuvirus KNV1 1.00 Acanthamoeba polyphaga moumouvirus 1.00 Acanthamoeba polyphaga mimivirus 1.00 Acanthamoeba castellanii mamavirus Fig. S11. Maximum likelihood phylogenetic tree of the concatenated major capsid protein and packaging ATPase genes, rooting with the DJR bacterial cluster II. The scale-bar indicates the average number of substitutions per site. Values on the branches represent transfer bootstrap expectation (TBE) support calculated by nonparametric bootstrap (1,000 replicates). The best-fit model was LG + F + R4, which was chosen according to Bayesian Information Criterion (BIC). The alignment has 92 sequences with 425 positions.

12 Phycisphaerae bacterium SM23_30 0.77 Nitrospirae bacterium GWB2_47_37 1.00 Magnetospirillum marisnigri Tree scale: 1 1.00 Magnetospirillum magneticum 0.79 Magnetospirillum sp. ME-1 0.87 Pseudoalteromonas virus PM2 0.77 Burkholderia ubonensis Kiloniella spongiae Concatenated 0.97 1.00 Thioclava dalianensis

0.91 Autolykiviridae_1.249.A cluster I Autolykiviridae_1.008.O 1.00 Polintoviruses 0.81 Autolykiviridae_1.020.O DJR bacterial 1.00 Autolykiviridae_1.044.O 0.94 Autolykiviridae_1.080.O Sulfolobus turreted icosahedral virus 1 STIV 1.00 Sulfolobus turreted icosahedral virus 2 Candidatus Nitrososphaera evergladensis SR1 0.96 0.76 Candidatus Nitrososphaera gargensis Ga9.2 Pyrobaculum oguniense TE7 0.95 PM2 Archaeal virus DEEP AND17J 0.99 1.00 Methanococcus voltae A3 Archaeoglobus veneficus 0.96 1.00 Archaeal virus DEEP JUN17B Cellulomonas 1.00 Archaeal virus DEEP JUN17A Methanolacinia petrolearia

0.92 cluster 0.99 Methanofollis ethanolicus 0.90 Thermococcus barophilus Bam35 Thermococcus kodakarensis DJR archaeal 1.00 0.79 Palaeococcus ferrophilus 1.00 Thermococcus guaymasensis Toil 0.88 Thermococcus nautili 1.00 pTN3 Rhodococcus phage Toil 0.97 Streptomyces noursei ATCC 11455 PRD1 0.78 Gluconobacter phage GC1 1.00 Enterobacteria phage PRD1 1.00 Enterobacteria phage PR4 0.47 0.92 Enterobacteria phage PR3 Phycodnaviridae Sulfobacillus thermosulfidooxidans 1.00 Sulfobacillus acidophilus TPY Brevibacillus sp. CF112 0.97 Bacillus phage Bam35c Mimiviridae 1.00 1.00 Bacillus phage GIL16c Bacillus virus AP50 cluster II 1.00

1.00 Bacillus sp. AFS075034 DJR bacterial 0.51 Bacillus phage Wip1 0.84 Mimiviridae-related Bacillus flexus 0.93 Bacillus pumilus 0.70 1.00 Bacillus licheniformis Mollivirus Cafeteriavirus-dependent mavirus 1.00 Yellowstone Lake virophage 7 0.98 Organic Lake virophage 0.99 Yellowstone Lake virophage 6 Iridoviridae II 0.92 Qinghai Lake virophage 0.76 Dishui lake virophage 1 0.63 Yellowstone Lake virophage 5 0.80 Sputnik virophage Iridoviridae I 1.00 Zamilon virus Polinton_2_NV 1.00 1.00 Polinton_1_DY Polinton_1_TC 0.94 Ascoviridae Polinton_2_DR 0.90 1.00 Polinton_1_DR 0.86 Polinton_1_SP Marseilleviridae 1.00 Polinton_2_SP Trichoplusia ni ascovirus 2c 1.00 Spodoptera frugiperda ascovirus 1a 0.94 Invertebrate iridescent virus 6 0.99 0.97 Lavidaviridae Invertebrate iridovirus 25 DJR Lausannevirus 0.92 1.00 Marseillevirus marseillevirus 0.92 Melbournevirus 0.73 Red seabream iridovirus eukaryoviruses 0.98 Lymphocystis disease virus 1 0.52 1.00 Frog virus 3 Acanthocystis turfacea Chlorella virus Can0610SP 0.99 Paramecium bursaria Chlorella virus NE-JV-1 0.87 Yellowstone lake phycodnavirus 2 1.00 Yellowstone lake phycodnavirus 3 1.00 Ostreococcus tauri virus OtV5 0.94 Micromonas pusilla virus 12T 0.83 0.78 Bathycoccus sp. RCC1105 virus BpV2 Emiliania huxleyi virus 202 0.49 Mollivirus sibericum 0.88 Heterosigma akashiwo virus 01 Organic Lake phycodnavirus 1 0.91 1.00 Phaeocystis globosa virus 1.00 Hokovirus HKV1 0.98 Klosneuvirus KNV1 1.00 Acanthamoeba polyphaga moumouvirus 1.00 Acanthamoeba polyphaga mimivirus 1.00 Acanthamoeba castellanii mamavirus Fig. S12. Maximum likelihood phylogenetic tree of the concatenated major capsid protein and packaging ATPase genes, rooting with the DJR cluster I. The scale-bar indicates the average number of substitutions per site. Values on the branches represent transfer bootstrap expectation (TBE) support calculated by nonparametric bootstrap (1,000 replicates). The best-fit model was LG + F + R4, which was chosen according to Bayesian Information Criterion (BIC). The alignment has 92 sequences with 425 positions.

13 Phycisphaerae bacterium SM23_30 0.77 Nitrospirae bacterium GWB2_47_37 1.00 Magnetospirillum marisnigri Tree scale: 1 1.00 Magnetospirillum magneticum 0.79 Magnetospirillum sp. ME-1 0.87 Pseudoalteromonas virus PM2 0.77 Burkholderia ubonensis Concatenated Kiloniella spongiae 0.97 1.00

Thioclava dalianensis cluster I 0.91 Autolykiviridae_1.249.A

Autolykiviridae_1.008.O DJR bacterial 0.70 1.00 Polintoviruses 0.81 Autolykiviridae_1.020.O 1.00 Autolykiviridae_1.044.O 0.94 Autolykiviridae_1.080.O Sulfolobus turreted icosahedral virus 1 STIV 1.00 Sulfolobus turreted icosahedral virus 2 Candidatus Nitrososphaera evergladensis SR1 0.96 0.76 Candidatus Nitrososphaera gargensis Ga9.2 Pyrobaculum oguniense TE7 PM2 0.95 Archaeal virus DEEP AND17J 0.99 1.00 Methanococcus voltae A3 Archaeoglobus veneficus Cellulomonas 0.96 1.00 Archaeal virus DEEP JUN17B 1.00 Archaeal virus DEEP JUN17A Methanolacinia petrolearia 0.92 cluster 0.99 Methanofollis ethanolicus Bam35 0.90 Thermococcus barophilus Thermococcus kodakarensis DJR archaeal 1.00 0.79 Palaeococcus ferrophilus 1.00 Thermococcus guaymasensis Toil 0.88 Thermococcus nautili 1.00 pTN3 Rhodococcus phage Toil PRD1 0.97 Streptomyces noursei ATCC 11455 0.78 Gluconobacter phage GC1 1.00 Enterobacteria phage PRD1 1.00 Enterobacteria phage PR4 0.47 Phycodnaviridae 0.92 Enterobacteria phage PR3 Sulfobacillus thermosulfidooxidans 1.00 Sulfobacillus acidophilus TPY Brevibacillus sp. CF112 0.97 Mimiviridae Bacillus phage Bam35c 1.00 1.00 Bacillus phage GIL16c Bacillus virus AP50 cluster II 1.00

1.00 Bacillus sp. AFS075034 DJR bacterial Mimiviridae-related 0.51 Bacillus phage Wip1 0.84 Bacillus flexus 0.93 Bacillus pumilus 1.00 Bacillus licheniformis Mollivirus Cafeteriavirus-dependent mavirus 1.00 Yellowstone Lake virophage 7 0.98 Organic Lake virophage Iridoviridae II 0.99 Yellowstone Lake virophage 6 0.92 Qinghai Lake virophage 0.76 Dishui lake virophage 1 0.63 Yellowstone Lake virophage 5 Iridoviridae I 0.80 Sputnik virophage 1.00 Zamilon virus Polinton_2_NV 1.00 1.00 Polinton_1_DY Ascoviridae Polinton_1_TC 0.94 Polinton_2_DR 0.90 1.00 Polinton_1_DR 0.86 Polinton_1_SP Marseilleviridae 1.00 Polinton_2_SP Trichoplusia ni ascovirus 2c 1.00 Spodoptera frugiperda ascovirus 1a Lavidaviridae 0.94 Invertebrate iridescent virus 6 0.99 0.97 Invertebrate iridovirus 25 DJR Lausannevirus 0.92 1.00 Marseillevirus marseillevirus 0.92 Melbournevirus 0.73 Red seabream iridovirus eukaryoviruses 0.98 Lymphocystis disease virus 1 0.52 1.00 Frog virus 3 Acanthocystis turfacea Chlorella virus Can0610SP 0.99 Paramecium bursaria Chlorella virus NE-JV-1 0.87 Yellowstone lake phycodnavirus 2 1.00 Yellowstone lake phycodnavirus 3 1.00 Ostreococcus tauri virus OtV5 0.94 Micromonas pusilla virus 12T 0.83 0.78 Bathycoccus sp. RCC1105 virus BpV2 Emiliania huxleyi virus 202 0.49 Mollivirus sibericum 0.88 Heterosigma akashiwo virus 01 Organic Lake phycodnavirus 1 0.91 1.00 Phaeocystis globosa virus 1.00 Hokovirus HKV1 0.98 Klosneuvirus KNV1 1.00 Acanthamoeba polyphaga moumouvirus 1.00 Acanthamoeba polyphaga mimivirus 1.00 Acanthamoeba castellanii mamavirus 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. The scale-bar indicates the average number of substitutions per site. Values on the branches represent transfer bootstrap expectation (TBE) support calculated by nonparametric bootstrap (1,000 replicates). The best-fit model was LG + F + R4, which was chosen according to Bayesian Information Criterion (BIC). The alignment has 92 sequences with 425 positions.