Candidatus Geothermarchaeota archaeon ex4572_27 archaeon Geothermarchaeota Candidatus
Methanothermococcus okinawensis
Methanocaldococcus bathoardescens
Candidatus Nanobsidianus stetteri Nanobsidianus Candidatus
Candidatus Nanobsidianus stetteri Nanobsidianus Candidatus
Methanocaldococcus fervens AG86 Methanothermococcus okinawensis
Methanocaldococcus bathoardescens
Methanocaldococcus sp. FS406-22
Methanocaldococcus fervens AG86
Methanocaldococcus jannaschii Methanocaldococcus sp. FS406-22 Methanocaldococcus fervens
Methanocaldococcus villosus Methanocaldococcus infernus Methanocaldococcus villosus 5 Hrk pendens Thermofilum Nanoarchaeum equitans Kin4-M Methanocaldococcus jannaschii Methanocaldococcus fervens Methanocaldococcus vulcanius
Thermofilum Thermofilum sp. ex4484_82 Methanocaldococcus villosus MethanocaldococcusMethanocaldococcus infernus villosus
Fervidobacterium thailandenseMethanopyrus sp. KOL6 Methanocaldococcus vulcanius Thermococcales archaeon 44_46 Methanopyrus kandleri Thermococcales archaeon 44_46 Methanotorris formicicus Fervidobacterium thailandense
Methanotorris igneus Methanothermus fervidus Methanothermus fervidus Methanotorris formicicus
Thermofilum
Methanotorris igneus Thermococcus sp. PK Thermococcus litoralis Thermococcus sp. 2319x1 Thermococcus sp. PK Thermosipho africanus Thermococcus litoralis Thermosipho atlanticus Candidatus Korarchaeota archaeon ThermococcusThermococcus sp. 2319x1 litoralis Thermococcus sp. 40_45 Thermococcus litoralis
Spirochaetes bacterium GWB1_36_13 Thermococcus sp. 40_45 Thermococcus sibiricus Thermotoga sp. 4484_232 Thermotoga sp. SG1 Thermotoga sp. KOL6Thermotoga neapolitana
Thermofilum uzonense Thermococcus sibiricus Thermofilum uzonense Thermotoga neapolitana LA10 Thermococcus sibiricus Thermofilum sp. NZ13 Thermotoga sp. RQ7 Candidatus Marsarchaeota G2 archaeon OSP_D Thermofilum pendens Candidatus Marsarchaeota G2 archaeon ECH_B_SAG-C16 CandidatusCandidatus Marsarchaeota Marsarchaeota G1 archaeon BE_DG1 archaeon OSP_D Candidatus Marsarchaeota CandidatusG2 archaeon ECH_B_SAG-F08 Marsarchaeota G2 archaeon ECH_B_2 Candidatus Marsarchaeota G2 archaeon ECH_B_3 Thermotoga naphthophila Thermococcus sibiricus Thermotoga petrophila MethanopyrusMethanopyruskandleri sp. KOL6 Thermococcus sp. EP1 Thermotoga sp. RQ2 Thermococcus barophilus Thermotoga maritima ThermotogaThermotoga sp. Mc24 Thermococcus celericrescens Thermococcus sp. EP1 Candidatus Korarchaeota archaeon Thermococcus barophilus Thermotoga sp. Cell2 Thermococcus barophilus Thermococcus paralvinellae Aciduliprofundum sp. MAR08-339 Thermococcus celericrescens Candidatus Korarchaeum cryptofilum OPF8 Thermotoga Thermococcus barophilus Candidatus Korarchaeum cryptofilum Thermotoga sp. TBYP3.1.4.1 Thermococcus paralvinellae AciduliprofundumCandidatus boonei Bathyarchaeota archaeon B24-2 Thermotoga sp. TBXY761 Aciduliprofundum booneiArchaeoglobus sulfaticallidus Aigarchaeota archaeon NZ13_MG1 Thermococcus sp. 4557 Caldanaerobacter subterraneus DictyoglomusCaldanaerobacter sp. NZ13-RE01 subterraneus Caldanaerobacter subterraneus Thermococcus sp. 4557 Thermococcus profundus Thermococcus profundus Archaeoglobus fulgidus Thermococcus siculi Caldicellulosiruptor morganii Archaeoglobus fulgidus Caldicellulosiruptor danielii Archaeoglobus fulgidus DSM 4304 Thermococcus pacificus Caldicellulosiruptor saccharolyticus Archaeoglobus fulgidus DSM 4304 Caldicellulosiruptor sp. F32 Geoglobus acetivorans ThermococcusThermococcus radiotolerans cleftensis Caldicellulosiruptor naganoensis ThermococcusThermococcus pacificus siculi Geoglobus ahangari Caldicellulosiruptor hydrothermalis Thermococcus cleftensis Ferroglobus placidus Caldicellulosiruptor owensensis Thermococcus radiotolerans Archaeoglobus profundus Thermococcus piezophilus Caldicellulosiruptor kronotskyensis Archaeoglobus veneficus Thermococcus sp. 5-4 Caldicellulosiruptor obsidiansis Thermococcus onnurineus Caldicellulosiruptor kristjanssonii Thermococcus piezophilus Caldicellulosiruptor lactoaceticus Thermococcus sp. 5-4 Caldicellulosiruptor acetigenus ThermococcusThermococcus thioreducens barossii Caldicellulosiruptor bescii Thermococcus onnurineus Caldicellulosiruptor bescii Caldicellulosiruptor bescii ThermococcusThermococcus thioreducens barossii Candidatus Geothermarchaeota archaeon ex4572_27 Thermococcus sp. P6 Thermofilum sp. ex4484_82 Thermofilum Thermococcus peptonophilus Thermofilum pendens Hrk 5 Thermococcus celer Thermofilum pendens Thermococcus kodakarensis Thermococcus sp. P6 Thermofilum sp. NZ13 Thermococcus peptonophilus Thermofilum uzonense Thermococcus gorgonarius Thermococcus celer Thermofilum uzonense Thermococcus kodakarensis Spirochaetes bacterium GWB1_36_13
Thermococcus zilligii Thermococcus gorgonarius Thermococcus sp. EXT12c Candidatus Nanobsidianus stetteri Thermococcus eurythermalis NanoarchaeumCandidatus equitans Kin4-M Nanobsidianus stetteri Thermosipho africanus Thermococcus zilligii Thermotoga sp. 4484_232 Candidatus Korarchaeota archaeon Thermococcus sp. EXT12c Thermosipho atlanticus ThermococcusThermococcus guaymasensis nautili Candidatus Korarchaeum cryptofilum OPF8 Thermococcus eurythermalis Thermococcus gammatolerans Candidatus Korarchaeum cryptofilum Thermotoga sp. KOL6 Aciduliprofundum sp. MAR08-339 Thermotoga sp. SG1 ThermococcusThermococcus gammatolerans nautili Thermotoga neapolitana Tree scale: 1 Thermococcus sp. AM4 Aciduliprofundum boonei Thermotoga neapolitana LA10 Aciduliprofundum boonei Thermotoga sp. RQ7 Palaeococcus pacificus Thermococcus sp. AM4 Archaeoglobus sulfaticallidus Thermococcus guaymasensis Thermotoga naphthophila Palaeococcus ferrophilus Tree scale: 1 Thermotoga petrophila Archaeoglobus fulgidus Thermotoga sp. RQ2 Pyrococcus yayanosii Archaeoglobus fulgidus Thermococcus chitonophagus Palaeococcus pacificus Thermotoga maritima Archaeoglobus fulgidus DSM 4304 Thermotoga Archaeoglobus fulgidus DSM 4304 Palaeococcus ferrophilus Thermotoga sp. Mc24 Candidatus Bathyarchaeota archaeon B24-2 Pyrococcus kukulkanii Thermotoga sp. Cell2 Aigarchaeota archaeon NZ13_MG1 Pyrococcus sp. ST04 Pyrococcus yayanosii Thermotoga Geoglobus acetivorans Thermotoga sp. TBYP3.1.4.1 Pyrococcus sp. NA2 Pyrococcus sp. NA2 Geoglobus ahangari Thermotoga sp. TBXY761 Pyrococcus abyssi Ferroglobus placidus Pyrococcus abyssi Pyrococcus horikoshii Archaeoglobus profundus Pyrococcus horikoshii Archaeoglobus veneficus Dictyoglomus sp. NZ13-RE01 Pyrococcus furiosus Thermococcus chitonophagus Caldanaerobacter subterraneus Pyrococcus furiosus DSM 3638 Caldanaerobacter subterraneus Pyrococcus kukulkanii Caldanaerobacter subterraneus Pyrococcus sp. ST04 Caldicellulosiruptor morganii Desulfurococcales archaeon ex4484_217_2 Pyrococcus furiosus Caldicellulosiruptor danielii Candidatus Kryptonium thompsoni Caldicellulosiruptor saccharolyticus Candidatus Kryptonium thompsoni Pyrococcus furiosus DSM 3638 Caldicellulosiruptor sp. F32 Candidatus Kryptobacter tengchongensis Caldicellulosiruptor naganoensis Candidatus Kryptobacter tengchongensis Caldicellulosiruptor hydrothermalis Candidatus Kryptobacter tengchongensis Candidatus Kryptobacter tengchongensis Caldicellulosiruptor owensensis Caldicellulosiruptor kronotskyensis Caldicellulosiruptor bescii Candidatus Korarchaeota archaeon Caldicellulosiruptor bescii Caldicellulosiruptor bescii Candidatus Marsarchaeota G1 archaeon BE_D Caldicellulosiruptor obsidiansis Candidatus Marsarchaeota G1 archaeon OSP_D Caldicellulosiruptor kristjanssonii Candidatus Marsarchaeota G2 archaeon ECH_B_SAG-F08 Caldicellulosiruptor lactoaceticus Candidatus Marsarchaeota G2 archaeon OSP_D Caldicellulosiruptor acetigenus Candidatus Marsarchaeota G2 archaeon ECH_B_SAG-C16 Candidatus Marsarchaeota G2 archaeon ECH_B_2 Candidatus Marsarchaeota G2 archaeon ECH_B_3
Thermocladium sp. ECH_B Caldivirga maquilingensis Topoisomerase:Methanosarcina barkeri str. Fusaro Caldivirga sp. MU80 Topoisomerase:Rhodopseudomonas palustris BisB18 Topoisomerase:Methanosarcina mazei Go1 Topoisomerase:Agrobacterium fabrum str. C 58 Topoisomerase:Methanosarcina acetivorans C 2A Vulcanisaeta thermophila Vulcanisaeta sp. EB80 Topoisomerase:Rhodobacter sphaeroides ATC C 17025 Topoisomerase:Methanococcoides burtonii DSM 6242 Desulfurococcales archaeon ex4484_217_2 Topoisomerase:Methanosaeta thermophila PT Vulcanisaeta distributa Topoisomerase:Geobacter sulfurreducens PC A Vulcanisaeta moutnovskia Topoisomerase:Halobacterium sp. NRC -1 Topoisomerase:Synechococcus sp. C C 9902 Candidatus Kryptonium thompsoni Topoisomerase:Methanospirillum hungatei JF-1 Thermoproteus tenax Candidatus Kryptonium thompsoni Thermoproteus uzoniensis Topoisomerase:Trichodesmium erythraeum IMS101 Candidatus Kryptobacter tengchongensis Topoisomerase:Picrophilus torridus DSM 9790 Thermoproteus sp. JCHS_4 Candidatus Kryptobacter tengchongensis Topoisomerase:Thermoplasma volcanium GSS1 Pyrobaculum arsenaticum DSM 13514 Topoisomerase:Synechocystis sp. PC C 6803 substr. Kazusa Candidatus Kryptobacter tengchongensis Topoisomerase:Archaeoglobus fulgidus DSM 4304 Pyrobaculum oguniense TE7 Topoisomerase:Haemophilus influenzae R2866 Topoisomerase:Escherichia coli C FT073 Candidatus Kryptobacter tengchongensis Pyrobaculum islandicum Topoisomerase:Vibrio cholerae MO10 Pyrobaculum calidifontis JCM 11548 Pyrobaculum aerophilum str. IM2 Topoisomerase:Bacillus cereus G9241 Thermocladium sp. ECH_B Caldivirga maquilingensis Topoisomerase:Methanosarcina mazei Go1 Pyrobaculum ferrireducens Pyrobaculum neutrophilum V24Sta Caldivirga sp. MU80 Topoisomerase:Methanosarcina acetivorans C 2A Pyrobaculum sp. WP30 Topoisomerase:CTopoisomerase:Aquifex lostridium perfringens str. aeolicus 13 VF5 Vulcanisaeta thermophila Topoisomerase:Methanosarcina barkeri str. Fusaro Candidatus Bathyarchaeota archaeon B24 Vulcanisaeta sp. EB80 Candidatus Bathyarchaeota archaeon ex4484_135 Vulcanisaeta distributa Topoisomerase:MethanococcoidesTopoisomerase:Thermofilum burtonii DSMpendens 6242 Hrk 5 Vulcanisaeta moutnovskia Topoisomerase:Pyrobaculum aerophilum str. IM2 Thaumarchaeota archaeon ex4484_121 Thermoproteus tenax Thermosulfidibacter takaii archaeon HR02 Thermodesulfobacterium sp. 37_54 Thermoproteus uzoniensis Candidatus Caldiarchaeum subterraneum Thermodesulfobacterium commune Thermoproteus sp. JCHS_4 Candidatus PacearchaeotaCandidatus Caldiarchaeum archaeon ex4484_31 subterraneum Topoisomerase:Methanococcus maripaludis S2 Pyrobaculum arsenaticum DSM 13514 Thermodesulfobacterium thermophilum Pyrobaculum oguniense TE7 Topoisomerase:Pyrococcus abyssi GE5 Thermodesulfobacterium hveragerdense Pyrobaculum calidifontis JCM 11548 Topoisomerase:Methanocaldococcus jannaschii DSM 2661 Thermodesulfobacterium geofontis Pyrobaculum aerophilum str. IM2 Topoisomerase:Thermococcus kodakarensis KOD1 Topoisomerase:Rubrobacter xylanophilus DSM 9941 Pyrobaculum ferrireducens Topoisomerase:SulfolobusTopoisomerase:Aeropyrum solfataricusTopoisomerase:Methanopyrus pernix P2 K1 kandleri AV19 Thermus thermophilus Thermodesulfobacterium geofontis Thermus thermophilus Pyrobaculum islandicum Thermus thermophilus Pyrobaculum neutrophilum V24Sta Topoisomerase:Methanothermobacter thermautotrophicus str. Delta H Thermodesulfobacterium sp. 37_54 NitratiruptorThermus sp. SB155-2 thermophilus Caldimicrobium thiodismutans Pyrobaculum sp. WP30 Nitratiruptor tergarcus Thermodesulfobacterium commune ThermodesulfobacteriumCaldimicrobium hydrogeniphilum thiodismutans CandidatusCandidatus Bathyarchaeota Bathyarchaeota archaeon archaeon ex4484_135 B24 Thermosulfurimonas dismutans Lebetimonas natsushimae Aquifex aeolicus Caminibacter mediatlanticus Thermodesulfatator indicus Thermodesulfobacterium hveragerdense Persephonella marina ThermodesulfobacteriumThermodesulfobacterium thermophilum geofontis Aquifex aeolicus Persephonella hydrogeniphilaCaldisericum exile ThermodesulfatatorAmmonifex autotrophicus degensii Thaumarchaeota archaeon ex4484_121 Persephonella sp. KM09-Lau-8Caldisericum exileNautilia profundicola Aquifex aeolicus Persephonella sp. IF05-L8 Thermodesulfobacterium geofontis Hydrogenivirga sp. 128-5-R1-1 Caldisericum exile ThermodesulfatatorAquifex atlanticus aeolicus VF5 archaeon HR02 Caldimicrobium thiodismutans Thermosulfurimonas dismutansAmmonifex Aquifexdegensii aeolicus VF5 Candidatus Pacearchaeota archaeon ex4484_31 CaldimicrobiumThermodesulfatator thiodismutans indicus Fervidobacterium pennivorans Candidatus Caldiarchaeum subterraneum Sulfurihydrogenibium yellowstonense Sulfurihydrogenibium Sulfurihydrogenibium sp. YO3AOP1 sp. Sulfurihydrogenibium Fervidobacterium pennivorans Fervidobacterium islandicum Fervidobacterium changbaicum Candidatus Caldiarchaeum subterraneum Dictyoglomus thermophilumFervidobacterium nodosum Fervidobacterium sp. SC_NGM5_G05 Dictyoglomus turgidum Thermodesulfobacterium hydrogeniphilum Dictyoglomus turgidum ThermodesulfatatorThermodesulfatator autotrophicus atlanticus Hydrogenivirga sp. 128-5-R1-1 bacterium HR17 bacterium HR17 Thermotoga sp. 50_64 Hydrogenivirga sp. 128-5-R1-1 Thermotoga sp. 50_64 Hydrogenobaculum Thermotoga caldifontis Thermotoga caldifontis Thermus thermophilus bacterium HR37bacterium HR19 Thermus thermophilus bacterium HR35 Thermus thermophilus Pseudothermotoga hypogea Thermus thermophilus Lebetimonas natsushimae Pseudothermotoga hypogea bacterium HR37 Thermosulfidibacter takaii Caminibacter mediatlanticus
Aquifex aeolicus PersephonellaPersephonella hydrogeniphila marina Caldisericum exile Caldisericum exile bacterium HR19 Persephonella sp. KM09-Lau-8 Thermocrinis ruber Thermocrinis albus bacterium HR35 Persephonella sp. IF05-L8 Caldisericum exile Hydrogenivirga sp. 128-5-R1-1 Nitratiruptor sp. SB155-2 Nitratiruptor tergarcus Nautilia profundicola Desulfurobacterium indicum Thermocrinis sp. GBS
Pseudothermotoga thermarum Pseudothermotoga thermarum Fervidobacterium pennivorans Desulfurobacterium sp. TC5-1 nodosum Fervidobacterium pennivorans Fervidobacterium Fervidobacterium islandicum Fervidobacterium Thermovibrio ammonificans changbaicum Fervidobacterium Thermocrinis minervae
Desulfurobacterium atlanticum Desulfurobacterium indicum
Sulfurihydrogenibium sp. Desulfurobacterium sp. TC5-1 Thermocrinis ruber Thermocrinis albus Hydrogenobaculum sp. Hydrogenobaculum Thermocrinis sp. GBS DesulfurobacteriumThermovibrio atlanticum ammonificans
Thermodesulfovibrio aggregans Hydrogenobacterthermophilus Desulfurobacterium thermolithotrophum Thermodesulfovibrio aggregans Sulfurihydrogenibium azorense Thermocrinis minervae Hydrogenobacterhydrogenophilus
Sulfurihydrogenibium subterraneum
Desulfurobacterium thermolithotrophum
Sulfurihydrogenibium sp. Thermodesulfovibrio aggregans Hydrogenobaculum Dictyoglomusturgidum Thermodesulfovibrio aggregans Dictyoglomusturgidum Hydrogenobacter thermophilus
Hydrogenobaculumsp. Hydrogenobacter hydrogenophilus Sulfurihydrogenibium azorense
Dictyoglomus thermophilumDictyoglomus
Sulfurihydrogenibium subterraneum
Sulfurihydrogenibium sp. YO3AOP1
Sulfurihydrogenibium yellowstonense
Fervidobacterium sp. SC_NGM5_G05 SI Fig. 12. Phylogenetic reconstruction of RG dataset with TopR1-like and TopR2-like sequences removed. Bacterial or Archaeal topoisomerase sequences included as an outgroup. Branch labels show species source of RG sequence, with Archaea in blue and Bacteria in red; or topoisomerase source, with Archaea in purple, Bacteria in green.