Online Resource 3
Supplementary Figure Captions and Table
Supplementary Figure Captions
Fig. S1 Unrooted maximum likelihood phylogenetic tree of 78 DNA polymerase
sequences built using PhyML
The aligned sequences used to build the tree were derived 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. S2 Unrooted maximum likelihood phylogenetic tree of 78 DNA polymerase
sequences built using MEGA6
Numbers at the branch points indicate percent bootstrap values. (a) The tree was built
based on aligned sequences where gap-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 MEGA6 phylogenetic tree. Numbers at the branch points indicate percent
bootstrap values. Groups with bootstrap values <60% 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. S3 Phylogenetic tree constructed by Bayesian inference analysis using PhyloBayes
Tree was reconstructed based on an alignment where all gap-containing sites were
removed. The sequence names are those listed in Table S1.
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Table S1 Accession numbers of the 78 DNA polymerase sequences used in this study
Accession No.
Sequence names as used in 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
2
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
3
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
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Fig. S1
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Fig. S2a
6
Fig. S2b
Fig. S2c
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Fig. 3
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