Candidatus Bathyarc

Aigarchaeota archaeo

Candidatus Korarcha

Archaeoglobus sulfat

Candidatus Korarcha

Archaeoglobus fulgid

Archaeoglobus fulgid

Candidatus Korarcha Aciduliprofundum sp

haeota archaeon B24 Candidatus Nanobsid us s Candidatus Nanobsid

Archaeoglobus profu

s Aciduliprofundum bo Aciduliprofundum bo

_232

Archaeoglobus fulgid na Archaeoglobus fulgid

icus na LA10

m GWB1_36_13

eum cryptofilum OPF n NZ13_MG1 phila la Nanoarchaeum equita Methanocaldococcus Methanothermococcu

Methanocaldococcus icallidus Methanocaldococcus eum cryptofilum Methanocaldococcus 761 us DSM 4304 3.1.4.1 us DSM 4304 eota archaeon . MAR08-339 terraneus Methanocaldococcus ianus stetteri -2 terraneus Thermosipho atlantic ianus stetteri Thermosipho africanu 3-RE01 terraneus Methanocaldococcus

MethanocaldococcusMethanocaldococcus ndus organii

onei onei anielii

Geoglobus acetivoran Thermotoga sp. 4484 Geoglobus ahangari accharolyticus Methanocaldococcus Thermotoga sp. SG1 aganoensis us Thermotoga neapolita us Thermotoga sp. KOL6 Thermotoga sp. RQ7 Ferroglobus placidus Methanopyrus sp. KO Archaeoglobus venef Thermotoga neapolita p. F32

Spirochaetes bacteriu 8 Thermotoga naphtho Methanopyrus kandle ThermotogaThermotoga sp. RQ2 petrophi ydrothermalis ns Kin4-M Thermotoga maritimaThermotogaThermotoga sp. Cell2 sp. Mc24 wensensis s okinawensis sp. FS406-22 Thermotoga ronotskyensis Methanotorris formic bathoardescens fervens AG86 Thermotoga bsidiansis Candidatus Geotherm jannaschii Thermotoga sp. TBXY Methanotorris igneus Thermotoga sp. TBYP ristjanssonii ctoaceticus Caldanaerobacter sub fervens Caldanaerobacter sub cetigenus Caldanaerobacter sub Dictyoglomus sp. NZ1 escii Thermofilum uzonens villosus infernus villosus Caldicellulosiruptor m escii Thermofilum uzonens Caldicellulosiruptor d Caldicellulosiruptor s escii vulcanius Caldicellulosiruptor n Thermofilum pendensThermofilum sp. NZ13 L6 Caldicellulosiruptor s Caldicellulosiruptor h Thermofilum pendens ri Caldicellulosiruptor o Caldicellulosiruptor k Thermofilum sp. ex44 Caldicellulosiruptor o PyrobaculumPyrobaculum calidifo aerophi archaeota archaeon e icus Caldicellulosiruptor k Caldicellulosiruptor la Pyrobaculum ferrired Caldicellulosiruptor a Pyrobaculum neutrop Caldicellulosiruptor b Caldicellulosiruptor b Thermofilum e Caldicellulosiruptor b Tree scale: 1 e Pyrobaculum arsenat Pyrobaculum sp. WP3 Hrk 5 Pyrobaculum islandic Pyrobaculum ogunien ntis JCM 11548 lum str. IM2 84_82 x4572_27 ucens Thermoproteus sp. JC hilum V24Sta ilandense Thermoproteus uzoni idus icum DSM 13514 0 Thermoproteus tenax um Vulcanisaeta moutno se TE7 inellae HS_4 Vulcanisaeta distribu Fervidobacterium tha hilus ensis Vulcanisaeta sp. EB8 hilus Candidatus Marsarch Vulcanisaeta thermop Candidatus Marsarch Methanothermus ferv 1 Candidatus Marsarch us Caldivirga maquilinge vskia us ThermocladiumCaldivirga sp. E sp. MU80 _45 CandidatusCandidatus Marsarch Marsarch ta aeota G2 archaeon EC Thermococcus paralv 19x1 aeota G2 archaeon EC 0 Thermococcus barop is aeota G2 archaeon EC hila Thermococcus barop Thermococcus sp. EP is Candidatus Marsarch Thermococcus sibiric CH_Bnsis aeota G2 archaeon EC Thermococcus sibiric aeota G2 archaeon O aeon 44_46 Candidatus Marsarch Thermococcus sp. 40 H_B_SAG-C16H_B_3 Thermococcus sp. 23 Candidatus Korarcha H_B_2 i aeota G1 archaeon O Thermococcus litoral Thermococcus litoral DSM 3638 aeota G1 archaeonH_B_SAG-F08 BESP_D Thermococcus sp. PK Candidatus Kryptoba Thermococcales arch ii Candidatus Kryptoba eota archaeon SP_D Candidatus Kryptoba Pyrococcus yayanosi Pyrococcus furiosus cter tengchongensis _D Candidatus Kryptoba Pyrococcus furiosus cter tengchongensis Pyrococcus horikosh ii Candidatus Kryptoniucter tengchongensis Pyrococcus abyssi ophagus Candidatus Kryptoniucter tengchongensis Pyrococcus sp. NA2 ilus Pyrococcus sp. ST04 m thompsoni Pyrococcus kukulkan us ar m thompsoni Thermococcus chiton Palaeococcus ferroph asensis chaeon ex4484_217_2 Palaeococcus pacific 4 atolerans Thermococcus guaym ermalis Thermococcus sp. AM Thermococcus gamm i Thermococcus euryth T12c Thermococcus nautil Thermococcus sp. EX narius Topoisomerase:Metha Thermococcus zilligii arensis Thermococcus gorgo Topoisomerase:MethaTopoisomerase:Metha nophilus Topoisomerase:Metha nosarcina barkeri str. Thermococcus kodak Thermococcus pepto ducens nosarcinanosarcina acetivoran mazei Go1 Topoisomerase:HalobTopoisomerase:Methanococcoides burtonii Fusaro Thermococcus thiore Topoisomerase:Rubro s C2A Thermococcus celer acterium nosaetasp. NRC-1 thermophila DSM 6242 Thermococcus sp. P6 Topoisomerase:Methabacter xylanophilus D nsis PT Thermococcus clefte ineus Topoisomerase:Picro nospirillum hungateiSM 9941 Topoisomerase:Therm Thermococcus onnur hilus philus torridus DSM 9 JF-1 Thermococcus piezop oplasma volcanium G 790 Topoisomerase:Archa SS1 Thermococcus barossii eoglobus fulgidus DS 4 M 4304 Thermococcus sp. 5- Topoisomerase:Metha Thermococcus radiotolerans Topoisomerase:Metha nosarcina mazei Go1 Topoisomerase:Metha nosarcina acetivoran Thermococcus sp. 4557 nosarcina barkeri str. Fusaros C2A Topoisomerase:Methanococcoides burtonii DSM 6242 Thermococcus celericrescens Thermococcus profun Topoisomerase:Thermofilum pendens Hrk 5 dus aculum aerophilum str. IM2 Thermococcus pacifi Topoisomerase:Pyrob cus Thermococcus siculi

9 Topoisomerase:Methanopyrus kandleri AV1

Desulfurococcales ar s S2 chaeon ex4484_217_2 nococcus maripaludischii DSM 2661 Desulfurococcales ar Topoisomerase:Metha nocaldococcus janna lta H s KOD1 chaeon ex4484_217_1 Topoisomerase:Metha islandicus autotrophicus str.ococcus De kodakarensi nothermobacter therm occus abyssi GE5 Ignicoccus hospitalis Topoisomerase:Therm Topoisomerase:Metha Topoisomerase:Pyroc Ignicoccus hospitalis KIN4/I lobus solfataricus P2 yrum pernix K1 Topoisomerase:Sulfo Desulfurococcales ar Topoisomerase:Aerop chaeon ex4484_42 aggreganarchaeon NZ3(B) Desulfurococcaceae Desulfurococcaceae s DSM 17230 pernix K1 archaeon AG1 ATCC 17025 Aeropyrum camini SY archaeon AG1 tris BisB1858 PCA obacter sphaeroides Pyrolobus fumarii opseudomonas palus Hyperthermus butylic acterium acterfabrum sulfurreducens str. C 2 Topoisomerase:Rhod Pyrodictium delaneyi 1 = JCM 12091 Topoisomerase:Rhod IMS101 Pyrodictium delaneyi Topoisomerase:Agrob Topoisomerase:Geobchococcus sp. CC990 866 Pyrodictium occultum us 03 substr. Kazusa Pyrodictium occultum odesmium erythraeum Topoisomerase:Syne cholerae MO10 chocystis sp. PCCophilus 68 erichiainfluenzae coli R2CFT073 r. 13 Topoisomerase:Trich lus cereus G9241 Thermogladius calde Desulfurococcales ar mar Topoisomerase:SyneTopoisomerase:HaemTopoisomerase:EschTopoisomerase:Vibrio ex aeolicus VF5 ridium perfringens st Staphylothermus hell Topoisomerase:Bacil Thermosphaera aggre rae chaeon ex4484_58 muc Topoisomerase:Aquif inus Topoisomerase:Clost Desulfurococcus muc enicus Desulfurococcus amy Desulfurococcus amy gans Desulfurococcus amy Fervidicoccus sp. osus Fervidicoccus fontis Fervidicoccus fontis osus lolyticus ium commune lolyticus ium sp. 37_54 lolyticus

ium thermophilum Kam940 Thermodesulfobacterium hveragerdenseium geofontis Metallosphaera yellow Thermodesulfobacter ium geofontis MetallosphaeraMetallosphaera sedul cupri ismutans Thermodesulfobacter dismutansdicus Metallosphaera hakon ium hydrogeniphilumismutans Acidianus brierleyi ThermodesulfobacterThermodesulfobacter Sulfolobales archaeo utotrophicustlanticus Sulfolobales archaeo Thermodesulfobacter AcidianusCandidatus hospitalis Acidianus stonensis Caldimicrobium thiod Acidianus hospitalis 8-5-R1-1 a na ThermosulfurimonasThermodesulfatator in Aquifex aeolicus Acidianus manzaensi ThermodesulfobacterCaldimicrobium thiod Acidianus sulfidivora ensis Ammonifex degensii Aquifex aeolicus VF5 n AZ1 ThermodesulfatatorThermodesulfatator a a 4 is SulfurisphaeraSulfolobus tokod sp. JCM 1 ypogea n AZ1 akaii Sulfolobus acidocald copahuensis SulfolobusSulfolobus acidocald sp. SCGC Hydrogenivirga sp. 12 Sulfolobus acidocald Sulfolobus acidocald ermarum s Sulfolobus sp. A20 Sulfolobus solfataricu ns Sulfolobus islandicus bacterium HR17 p. TC5-1 Sulfolobus islandicus Sulfolobales archaeo Thermotoga sp. 50_6 ndicum Sulfolobus islandicus Thermotoga caldifont Sulfolobus islandicus Pseudothermotoga h ificans Sulfolobus islandicus tlanticum Sulfolobus islandicus aii 6833 Sulfolobus islandicus Sulfolobus islandicus Thermosulfidibacter t Sulfolobus islandicus Sulfolobus islandicus Aciduliprofundum sp bacterium HR19 5-L8 Sulfolobus islandicus arius DSM 639 bacterium HR35 AB-777_G05 bacterium HR37 09-Lau-8 arius SUSAZ Pseudothermotoga th arius DSM 639 eniphila arius Candidatus Bathyarc s hermolithotrophum 5-2 Candidatus Bathyarc Desulfurobacterium s Candidatus Pacearch Desulfurobacterium i s n SCGC AB-777_J03 HVE10/4 DesulfurobacteriumThermovibrio a ammon Aquifex aeolicus Thaumarchaeota arch

imae archaeon HR02

Hydrogenivirga sp. 12 . anticus e s PersephonellaPersephonella sp. IF0 marina s s Candidatus Caldiarch Candidatus Caldiarch s

Persephonella sp. KM Dictyoglomus thermo Fervidobacterium cha Fervidobacterium pen Dictyoglomus turgidu Fervidobacterium isla Fervidobacterium sp. Fervidobacterium pen Fervidobacterium nod

Persephonella hydrog m

sp. Desulfurobacterium t Nitratiruptor tergarcu haeota archaeon ex44 Nitratiruptor sp. SB15 rmophilus haeota archaeon B24

rogenophilus aggregans Caldisericum exile azorense aggregans aeota archaeon ex448 Caldisericum exile

Nautilia profundicola Caldisericum exile p. Thermocrinis ruber sp.YO3AOP1 Thermocrinis albus

subterraneum Lebetimonas natsush yellowstonense aeon ex4484_121 Thermocrinis sp. GBS Caminibacter mediatl

Thermus thermophilu Thermocrinis minerva Thermus thermophilu 8-5-R1-1 Thermus thermophilu aeum subterraneum Thermus thermophilu aeum subterraneum

philum

SC_NGM5_G05 ngbaicum ndicum m nivorans nivorans

osum

Dictyoglomus turgidu

Sulfurihydrogenibium 84_135 Hydrogenobacter the

Hydrogenobaculum Thermodesulfovibrio Hydrogenobacter hyd 4_31 Thermodesulfovibrio Sulfurihydrogenibium

Hydrogenobaculum s

Sulfurihydrogenibium

Sulfurihydrogenibium

Sulfurihydrogenibium SI Fig. 13. Phylogenetic reconstruction of RG dataset with TopR2-like sequences removed. Bacterial and Archaeal topoisomerase sequences included as an outgroup. Branch labels show source of RG sequence, with in blue and Bacteria in red; or topoisomerase source, with Archaea in purple, Bacteria in green.