Online Resource 3
Supplementary Figure Captions and Table
Supplementary Figure Captions
Fig. S1Unrooted maximum likelihood phylogenetic tree of 78 DNA polymerase sequences built using PhyML
The aligned sequences used to build the tree werederived from the full-length one where columns with >10% gaps were removed. Numbers at the branch points indicate percent bootstrap values. This tree is unrooted.
Fig. S2Unrooted maximum likelihood phylogenetic tree of 78 DNA polymerase sequences built using MEGA6
Numbers at the branch pointsindicate percent bootstrap values. (a) The tree was built based on aligned sequences wheregap-containing sites were removed, except for polymerase domains (I, II, III, IV, V, VI, and VII) conserved among B-family DNA polymerases.The sequence names are those listed in Table S1.(b) Schematic representation of Homo sapiens DNA polymerase α showing the seven polymerase domains that were left after removing the gap-containing sites. The sequences used in the construction of phylogenetic tree contained 419 amino acid residues. (c)Summary of the MEGA6phylogenetic tree.Numbers at the branch points indicate percent bootstrap values. Groups with bootstrap values60% were not individually considered. α, eukaryotic pol-α; ε, eukaryotic pol-ε; δ, eukaryotic pol-δ; ζ, eukaryotic pol-ζ; AdenoV, adenoviruses; PoxV, poxviruses; ChlorellaV, chlorella viruses; MimiV, mimivirus; MegaV, megaviruses; PandoraV, pandoraviruses; and PithoV, pithovirus.
Fig. S3Phylogenetic tree constructed by Bayesian inference analysisusing PhyloBayes
Tree was reconstructed based on an alignment where all gap-containing sites were removed.The sequence names are those listed in Table S1.
Table S1 Accession numbers of the 78DNA polymerase sequences used in this study
Accession No. / Sequence names as usedin Figs.2a, 3, and Figs S2a, and S3.AFM52356 / B-family DNA polymerase partial Megavirus terra1
AFM52364 / B-family DNA polymerase partial Megavirus courdo5
AEX61758 / DNA polymerase Megavirus courdo7
YP_003986825 / DNA polymerase Acanthamoeba polyphaga mimivirus
YP_003970183 / putative DNA-dependent DNA polymerase family B Cafeteria roenbergensis virus BV-PW1
YP_008052566 / DNA polymerase Phaeocystis globosa virus
AGE58955 / DNA polymerase Paramecium bursaria Chlorella virus OR0704.2.2
AGE57130 / DNA polymerase Acanthocystis turfacea Chlorella virus NE-JV-3
YP_008436920 / B-family DNA polymerase Pandoravirus salinus
YP_008318996 / b-family DNA polymerase Pandoravirus dulcis
AAB67116 / DNA-dependent DNA polymerase homolog Feldmannia species virus
CAA43922 / DNA polymerase III calatytic subunit Saccharomyces cerevisiae
NP_001190611 / DNA polymerase delta subunit 1 Arabidopsis thaliana
XP_003864005 / DNA polymerase delta catalytic subunit putative Leishmania donovani
CAA61369 / DNA polymerase delta Drosophila melanogaster
XP_005991045 / PREDICTED: DNA polymerase delta catalytic subunit Latimeria chalumnae
AAA35768 / DNA polymerase delta Homo sapiens
NP_035261 / DNA polymerase delta catalytic subunit Mus musculus
YP_009000951 / DNA polymerase delta catalytic subunit Pithovirus sibericum
AAA46008 / polymerase Human herpesvirus 5
BAE19749 / DNA polymerase UL30 Human herpesvirus 1
YP_401712 / DNA polymerase Human herpesvirus 4
XP_003861052 / DNA polymerase zeta catalytic subunit putative Leishmania donovani
P14284 / RecName: Full DNA polymerase zeta catalytic subunit AltName: FullProtein Reversionless 3 (Saccharomyces cerevisiae)
BAC82450 / catalytic subunit of polymerase zeta Arabidopsis thaliana
AAG30224 / DNA polymerase zeta catalytic subunit Drosophila melanogaster
XP_005990939 / PREDICTED: DNA polymerase zeta catalytic subunit isoform X1 Latimeria chalumnae
AAG09402 / DNA polymerase zeta catalytic subunit variant 1 Homo sapiens
NP_035394 / DNA polymerase zeta catalytic subunit Mus musculus
P09884 / RecName: Full DNA polymerase alpha catalytic subunit AltName: Full DNA polymerase alpha catalytic subunit p180 (Homo sapiens)
NP_032918 / DNA polymerase alpha catalytic subunit Mus musculus
XP_006003459 / PREDICTED: DNA polymerase alpha catalytic subunit Latimeria chalumnae
NP_536736 / DNA polymerase alpha 180kD Drosophila melanogaster
NP_201511 / DNA polymerase alpha catalytic subunit Arabidopsis thaliana
AAC47538 / DNA polymerase alpha catalytic subunit Leishmania donovani
CAA90524 / DNA polymerase I Saccharomyces cerevisiae
YP_687101 / putative DNA-directed DNA polymerase B Methanocella arvoryzae MRE50
ACB07943 / DNA polymerase B region Candidatus Korarchaeum cryptofilum OPF8
WP_011011325 / DNA polymerase Pyrococcus furiosus
AAA72443 / DNA polymerase Methanococcus voltae
NP_614322 / B family DNA polymerase Methanopyrus kandleri AV19
WP_010878004 / DNA polymerase Archaeoglobus fulgidus
WP_011849732 / DNA polymerase Pyrobaculum calidifontis
WP_012186387 / DNA polymerase Caldivirga maquilingensis
WP_011752067 / DNA polymerase Thermofilum pendens
WP_011998098 / DNA polymerase Ignicoccus hospitalis
WP_011839179 / DNA polymerase Staphylothermus marinus
WP_011822063 / DNA polymerase Hyperthermus butylicus
WP_010902345 / DNA polymerase Halobacterium salinarum
NP_279569 / DNA polymerase B1 Halobacterium sp. NRC-1
YP_502623 / DNA polymerase B region Methanospirillum hungatei JF-1
NP_542554 / putative DNA-dependent DNA polymerase Halorubrum phage HF2
BAA75662 / DNA polymerase Aeropyrum pernix
AAB53090 / DNA polymerase Sulfolobus solfataricus P2
BAJ48658 / DNA polymerase I Candidatus Caldiarchaeum subterraneum
AAB94881 / DNA polymerase partial Cenarchaeum symbiosum
AFS82883 / DNA polymerase I Candidatus Nitrosopumilus sp.AR2
EGG42460 / DNA polymerase I Candidatus Nitrosoarchaeum limnia SFB1
NP_172303 / DNA polymerase epsilon catalytic subunit A Arabidopsis thaliana
XP_003865021 / DNA polymerase epsilon catalytic subunit putative Leishmania donovani
AAA88711 / DNA polymerase II Saccharomyces cerevisiae
NP_524462 / DNA polymerase epsilon Drosophila melanogaster
NP_035262 / DNA polymerase epsilon catalytic subunit A Mus musculus
NP_006222 / DNA polymerase epsilon catalytic subunit A Homo sapiens
XP_005993379 / PREDICTED: DNA polymerase epsilon catalytic subunit A Latimeria chalumnae
NP_048107 / ORF MSV036 putative DNA polymerase Choristoneura biennis entomopox virus DPOL homolog (vaccinia E9L) similar to SW:P30319 Melanoplus sanguinipes entomopoxvirus
NP_039057 / DNA polymerase Fowlpox virus
YP_004821396 / DNA polymerase Yoka poxvirus
NP_042094 / DNA polymerase Variola virus
AAB59829 / DNA polymerase Vaccinia virus
ADX22900 / DNA polymerase Monkeypox virus
NP_203396 / CUN091 putative dnapolymerase similar to AcMNPV ORF65 Culex nigripalpus nucleopolyhedrovirus
NP_148895 / ORF111 DNAPOL Cydia pomonella granulovirus
YP_025135 / DNA polymerase Neodiprion serifer nucleopolyhedrovirus
AGH58206 / polymerase Gull adenovirus
YP_004123738 / polymerase Murine adenovirus 2
ABK59062.1 / polymerase Human adenovirus 37
YP_006272954.1 / polymerase Chimpanzee adenovirus Y25
Fig. S1
Fig. S2a
Fig. S2b
Fig. S2c
Fig. 3
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