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Fig. S1. Schematic Representation of the Phylogenetic Relation Between the Thermococcales, the Methanococcales and Their Closest Archaeal Relatives

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Fig. S1. Schematic Representation of the Phylogenetic Relation Between the Thermococcales, the Methanococcales and Their Closest Archaeal Relatives Fig. S1. Schematic representation of the phylogenetic relation between the Thermococcales, the Methanococcales and their closest archaeal relatives. In this schema the different genus of the Thermococcales and the Methanococcales were coloured in blue and green respectively Original organisation before MGE integration tRNA Arg TK_RS02830 TK_RS03040 TK_RS01875 TK_RS02080 tRNA Glu ~ 150kb Integrations Original organisation after the multiple MGE integration tRNA TK_RS01880 Arg TK_RS02830 TK_RS02070 TK_RS03040 TK_RS01875 TKVA TK_RS02840 TK_RS02080tRNA TKVB TK_RS03035 Glu attLA attRA attLB attRB Inversion Organisation in the type strain genome tRNA TK_RS01880 TK_RS02070 TK_RS02830 Arg TK_RS03040 TK_RS01875 TKV2 tRNATK_RS02080 TK_RS02840 TKV3 TK_RS03035 Glu 320,075-122 347,135-87 499,291-338 526,817-69 attL2 attR2 attL3 attR3 Fig. S2. TKV2 and TKV3 inactivation by large DNA inversion in T. kodakarensis genome. 1 1 1 1 1 P P P I I P I 1 1 P I _ _ I _ P P _ 3 4 _ I I 6 1 6 2 1 1 9 1 5 _ _ 1 P 1 1 2 1 1 1 9 P 9 2 1 3 I P 0 1 8 - I I 1 P 1 P 7 0 P 7 P _ 0 E E 1 I 6 I P _ I I _ 0 1 i 1 2 4 4 _ 1 _ _ 1 0 _ 7 _ 1 1 2 _ 1 _ R 5 7 5 5 2 M 4 B 1 M M 2 5 1 S V V M V 1 A 2 l E E C H S H S M S C S A 7 H 6 7 V − o C X K O 1 1 F 1 3 2 F S G G C D C 6 D J N D N C C P C C a a a K V V E V V V p h a u a 2 e p u h p b a D g t i V M M i s M M M M M c G b K c g K s b k H s y l T M a T P T T T T T T T TPV1 TKV1 M p p Afu M M M M M M M M M M P P P P P Mva_IV1 Mok_IV1 MfeAG86_IV1 P Ta Tb Tc Td Te Tf Tg Th Ti Tj Tk Tl Tm Tn To Tp A C Ma B F Mb Mc Md Me Mf Mg Mh Mi Mj Mk Ml D E Ta PabGE2_IP1 Tb TGV1 Tc PHV1 Td PspNA2_IP1 Te PyaCH1_IP16 Tf PchGC74_IP1 Tg PkuNCB100_IP1 Th TbaCH5_E2 Ti TKV3 Tj TceDSM17994_IP1 Tk TguDSM11113_IP1 Tl pT26−2 Tm TKV2 Tn TspJCM11816_IP1 To PliDSM5473_IP1 Tp TbaCH5_E1 Ma MVV1 Mb MthDSM2095_IP1 Mc MigKol5_IP1 Md pMEFER01 Me MspFS406-22_IP1 Mf MMaKA1_IP1 Mg MMaOS7_IP1 Mh MMC7V2 Mi MMPV1 Mj MMC7V1 Mk MMaX1_iP1 Methanococcales virus 50 Ml MMC6V1 A TPV1 Methanococcales pT26-2 40 B Mva_IV1 C Afu Thermococcales pT26-2 30 D TKV1 E Mok_IV1 Thermococcales virus 20 F MfeAG86_IV1 Unknown 10 0 Number of BBH Fig. S3. Conservation of plasmids of the pT26-2and their connections with viruses by heatmap. Results of Bidirectional Best-Hit are represented as a heatmap. In the heatmap the number of conserved proteins is indicated in the scale. The heatmap analysis revealed two distinct groups, one containing the elements in Thermococcales and the other those of Methanococcales. The heatmap also show that some plasmid of the pT26-2 family shared genes with viruses. Protein group Core in 2 to 4 pT26-2-related plasmid Singleton Other Fig. S4. Size protein encoded by plasmids of the pT26-2 family. The protein set were divided in 4 different groups. For each group the density of protein is indicated at the different protein size. Fig. S5. Organisation of the pT26-2 putative replication protein and its comparison with other replication proteins. In this schematic representation the Primpol and the P-loop NTPase domain are indicated in green and blue respectively. KXA90124_candidate_divison_MSBL1_archaeon_SCGC_AAA259B11 98.6/100KXB04138_candidate_divison_MSBL1_archaeon_SCGC_AAA261G05 100/100 KUO41305_Hadesarchaea_archaeon_DG_33_1 96.1/99 KUO42083_Hadesarchaea_archaeon_YNP_N21 100/100KYC45172_Arc_I_group_archaeon_B03fssc0709_Meth_Bin005 96.4/100 KYC54749_Arc_I_group_archaeon_ADurb1013_Bin02101 KYK36871_1_Theionarchaea_archaeon_DG_70_1_no_comment 272844_MCM1_NP_127115_Pyrococcus_abyssi_GE5 65.1/82 98.6/10070601_MCM1_NP_142570_Pyrococcus_horikoshii_OT3 96.2/10096/100342949_MCM_shell_YP_004424138_Pyrococcus_sp_NA2 96.8/99186497_MCM1_NP_578211_Pyrococcus_furiosus_DSM_3638 529709_MCM1_YP_004623548_Pyrococcus_yayanosii_CH1 98.6/1001042877_MCM1_YP_004762586_Thermococcus_sp_4557 99.7/10090.8/100523850_MCM1_YP_002306424_Thermococcus_onnurineus_NA1 78/82 99.4/10069014_MCM1_YP_184033_Thermococcus_kodakarensis_KOD1 86.5/100246969_MCM1_YP_002582218_Thermococcus_sp_AM4 95.5/100593117_MCM1_YP_002960390_Thermococcus_gammatolerans_EJ3 100/100523849_MCM1_ZP_09730841_Thermococcus_litoralis_DSM_5473 73.4/99 604354_MCM1_YP_002994932_Thermococcus_sibiricus_MM_739 90.8/96 391623_MCM1_YP_004070279_Thermococcus_barophilus_MP Tbaro_E2_TBCH5v1_2333_ALM76228_1 97.1/100 100/100WP_011250312_TKV4_Thermococcus_kodakarensis_no_comment 30.3/90 WP_048151234_STIV_pTN3fam_Palaeococcus_ferrophilus_no_comment AEY69051_TPV1_Thermococcus_prieurii_virus_1_no_comment 92.4/88 98.7/100 WP_099209188_Thermococcus_sp_EXT12c_no_comment100/100 98.4/100 AGX15318_pTN3_plasmid_Thermococcus_nautili_no_comment 342949_MCM1_YP_004424245_PspNA2_MGE_Pyrococcus_sp_NA2 100/100 TKV1_TK0096_BAD84285_1 644295_MCM1_YP_003726351_Methanohalobium_evestigatum_Z_7303 12.9/76 224325_MCM1_NP_069353_Archaeoglobus_fulgidus_DSM_4304 99.5/100589924_MCM1_YP_003435419_Ferroglobus_placidus_DSM_10642 82.5/100693661_MCM1_YP_004340760_Archaeoglobus_veneficus_SNP6 98/99 AGK61979_Archaeoglobus_sulfaticallidus_PM70_1 572546_MCM1_YP_003400528_Archaeoglobus_profundus_DSM_5631 100/100 572546_MCM_shell_YP_003401418_Archaeoglobus_profundus_DSM_5631 99.9/100 572546_MCM_shell_YP_003400568_Archaeoglobus_profundus_DSM_5631 78.3/99188937_MCM_shell_NP_615641_Methanosarcina_acetivorans_C2A 100/100192952_MCM1_NP_633860_Methanosarcina_mazei_Go1 269797_MCM1_YP_305120_Methanosarcina_barkeri_str_Fusaro 55.8/74 679901_MCM1_YP_004615679_Methanosalsum_zhilinae_DSM_4017 28/97 97.1/100259564_MCM1_YP_567033_Methanococcoides_burtonii_DSM_6242 99.8/9488.3/97 547558_MCM1_YP_003541798_Methanohalophilus_mahii_DSM_5219 644295_MCM_shell_YP_003726241_Methanohalobium_evestigatum_Z_7303 188937_MCM1_NP_618700_Methanosarcina_acetivorans_C2A 990316_MCM1_YP_004385287_Methanosaeta_concilii_GP6 87.1/65 77.6/100 100/100 349307_MCM1_YP_842696_Methanosaeta_thermophila_PT 1110509_MCM1_AET65277_Methanosaeta_harundinacea_6Ac 84.7/98 100/100OFV66637_Candidatus_Syntrophoarchaeum_butanivorans 89.1/9295/100 OFV68247_Candidatus_Syntrophoarchaeum_caldarius PXF52786_ANME_1_cluster_archaeon 94.6/92 PPA79667_ANME_2_cluster_archaeon_HR1 95.8/100304371_MCM1_YP_003356305_Methanocella_paludicola_SANAE 100/1001041930_MCM1_YP_005381018_Methanocella_conradii_HZ254 351160_MCM1_YP_686686_Methanocella_arvoryzae_MRE50 86.9/75 410358_MCM1_YP_001030268_Methanocorpusculum_labreanum_Z 368407_MCM1_YP_001047160_Methanoculleus_marisnigri_JR1 98.8/9256.9/83 100/10057.8/99 882090_MCM1_ZP_09043156_Methanolinea_tarda_NOBI_1 58.7/100 521011_MCM1_YP_002467125_Methanosphaerula_palustris_E1_9c 97.5/10043.4/100456442_MCM1_YP_001404833_Methanoregula_boonei_6A8 90.6/99 323259_MCM1_YP_502454_Methanospirillum_hungatei_JF_1 937775_MCM1_ZP_09700740_Methanoplanus_limicola_DSM_2279 99.9/100679926_MCM1_YP_003894184_Methanolacinia_petrolearia_DSM_11571 OKY78610_Candidatus_Methanohalarchaeum_thermophilum 797209_MCM1_ZP_08042510_Haladaptatus_paucihalophilus_DX253 99.5/93 309800_MCM1_YP_003534297_Haloferax_volcanii_DS2 57.3/6495.9/100 87.8/100469382_MCM1_YP_004035124_Halogeometricum_borinquense_DSM_11551 98.9/100 362976_MCM1_YP_659323_Haloquadratum_walsbyi_DSM_16790 49.8/97756883_MCM1_YP_004809424_halophilic_archaeon_DL31 88.1/89 84.7/48 416348_MCM_shell_YP_002567153_Halorubrum_lacusprofundi_ATCC_49239 797210_MCM1_YP_004596122_Halopiger_xanaduensis_SH_6 21.1/84547559_MCM_shell_YP_003480325_Natrialba_magadii_ATCC_43099 100/10075.3/100797304_MCM_shell_ZP_08967542_Natronobacterium_gregoryi_SP2 89.8/78543526_MCM1_YP_003401890_Haloterrigena_turkmenica_DSM_5511 84.3/66 795797_MCM1_YP_003735228_Halalkalicoccus_jeotgali_B3 64.7/77 348780_MCM_shell_YP_331276_Natronomonas_pharaonis_DSM_2160 634497_MCM1_YP_004794671_Haloarcula_hispanica_ATCC_33960 99.9/100272569_MCM_shell_YP_137231_Haloarcula_marismortui_ATCC_43049 97.4/78 99.6/100 98.6/78 485914_MCM1_YP_003176874_Halomicrobium_mukohataei_DSM_12286 519442_MCM1_YP_003131067_Halorhabdus_utahensis_DSM_12940 93.3/78 1033806_MCM1_ZP_08560916_Halorhabdus_tiamatea_SARL4B 89.2/90 478009_MCM1_YP_001689961_Halobacterium_salinarum_R1 12.6/32 99.5/98 100/100751944_MCM1_ZP_09027959_Halobacterium_sp_DL1 99.4/100797303_MCM1_ZP_08964560_Natrinema_pellirubrum_DSM_15624 100/100 348780_MCM1_YP_327587_Natronomonas_pharaonis_DSM_2160 99.5/100 272569_MCM_shell_YP_136848_Haloarcula_marismortui_ATCC_43049 416348_MCM1_YP_002565410_Halorubrum_lacusprofundi_ATCC_49239 100/100 797304_MCM_shell_ZP_08968377_Natronobacterium_gregoryi_SP2 KYK28479_Thermoplasmatales_archaeon_SG8_52_1 98.6/100 WP_020449728_Candidatus_Methanomassiliicoccus_intestinalis 100/100WP_049796361_Methanomassiliicoccus_luminyensis 439481_MCM1_YP_003483546_Aciduliprofundum_boonei_T469 99.3/100 333146_MCM1_ZP_05571039_Ferroplasma_acidarmanus_fer1 82.9/100 99.9/100 31/90 263820_MCM1_YP_023995_Picrophilus_torridus_DSM_9790 100/100 EQB71237_Thermoplasmatales_archaeon_A_plasma 95.6/100 273075_MCM1_NP_394261_Thermoplasma_acidophilum_DSM_1728 100/100273116_MCM1_NP_111551_Thermoplasma_volcanium_GSS1 274854_MCM1_EHR75878_uncultured_marine_group_II_euryarchaeote 1072681_MCM1_ZP_09209841_Candidatus_Haloredivivus_sp_G17 99.5/100 KYK25047_Euryarchaeota_archaeon_SM23_78 91.8/100 PKM92164_Euryarchaeota_archaeon_HGW_Euryarchaeota_1 ODS38582_Candidatus_Altiarchaeales_archaeon_WOR_SM1_86_2 96.6/100 OYT42372_Candidatus_Altiarchaeales_archaeon_ex4484_43 99.7/100 PIX48385_Candidatus_Altiarchaeum_sp__CG_4_8_14_3_um_filter_33_2054 100/100OIQ05030_Candidatus_Altiarchaeum_sp__CG2_30_32_3053 0/76PIV27464_Candidatus_Altiarchaeum_sp__CG03_land_8_20_14_0_80_32_618 76.2/59 0/43PIN68127_Candidatus_Altiarchaeum_sp__CG12_big_fil_rev_8_21_14_0_65_33_22 PIZ30941_Candidatus_Altiarchaeum_sp__CG_4_10_14_0_8_um_filter_32_851
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