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LC-Locus Alignment Sites Distance, Number of Nodes Supplementary 12.5 10.0 7.5 5.0 Distance, number of nodes 2.5 0.0 g1 g2 g3 g3.5 g4 g5 g6 g7 g8 g9 g10 g10.1 g11 g12 g13 g14 g15 (11) (3) (3) (10) (3) (3) (3) (3) (3) (3) (3) (4) (3) (3) (3) (2) (3) LC-locus alignment sites Supplementary Figure S1. Compatibility of the evolutionary histories of the LC-locus and of individual LC genes.The sites of the LC-locus alignment are arranged along the X-axis, with the dashed red lines demarcating the alignment boundaries of the individual RcGTA-like genes (labeled with RcGTA gene names, g1 through g15; see Supplementary Table S4). For each alignment site, the Y-axis shows the phylogenetic distance between the optimal placement of a taxon in a phylogeny reconstructed from a 100 amino-acid window that surrounds the site and in the LC-locus phylogeny, averaged across all sliding windows that contain the site. The Y-axis values averaged across all taxa and all sites within a gene is shown in parentheses on the X-axis. For 15 out of 17 genes, only 2-4 nodes separate the optimal taxon position in the LC-locus and gene phylogeny. The inflated distances for g1 and g3.5 are likely because only 15 and 21 of 95 LCs, respectively, have a homolog of these genes and the SSPB analysis is highly sensitive to missing data (Berger et al. 2011). a. Bacteria Unassigned Thermotogae Tenericutes Synergistetes Spirochaetes Proteobacteria ylum Planctomycetes h p Firmicutes Deferribacteres Cyanobacteria Chloroflexi Bacteroidetes Actinobacteria Acidobacteria 1(11,750) 2(1,750) 3(2,538) 4(168) 5(51) 6(54) 7(43) 8(32) 9(26) 10(40) 11(33) 12(198) 13(173) 14(101) 15(98) 16(43) 17(114) Number of rcc01682−rcc01698 homologs in a cluster b. Proteobacteria Gammaproteobacteria Epsilonproteobacteria Deltaproteobacteria class Betaproteobacteria Alphaproteobacteria Acidithiobacillia 1(8,150) 2(1,669) 3(2,522) 4(163) 5(46) 6(53) 7(43) 8(32) 9(26) 10(39) 11(33) 12(196) 13(173) 14(101) 15(98) 16(43) 17(114) Number of rcc01682−rcc01698 homologs in a cluster c. Gammaproteobacteria Xanthomonadales Vibrionales Unassigned Thiotrichales Pseudomonadales Pasteurellales order Oceanospirillales Methylococcales Enterobacteriales Chromatiales Cellvibrionales Alteromonadales Aeromonadales 1(6,043) 2(1,200) 3(2,048) 4(22) 5(2) 6(1) 7(0) 8(0) 9(0) 10(0) 11(0) 12(0) 13(0) 14(0) 15(1) 16(0) 17(0) Number of rcc01682−rcc01698 homologs in a cluster 1 10 100 500 1,000 5,000 10,000 Supplementary Figure S2. Adjacency of the RcGTA structural homologs detected in genomes of (a) domain Bacteria, (b) phylum Proteobacteria, and (c) class γ-proteobacteria. For each panel, the variation of the observed cluster sizes (from 1 to 17 genes, arranged on the X-axis) is shown per taxonomic group (arranged on Y axis) with at least one detected RcGTA homolog. The diameter of each circle is scaled with respect to the number of genomes (same scale for all panels; see legend at the bottom of the panel c). The total number of genomes in each size category is shown in parentheses on the X-axis labels. Across bacteria, the clusters with at least nine RcGTA homologs are found predominantly in α-proteobacteria; the exceptions from other taxonomic groups are shown in orange. Brucella melitensis M28 Brucella melitensis M5-90 Brucella melitensis NI Brucella melitensis ATCC 23457 Brucella abortus S19 Brucella abortus 2308 Brucella abortus bv. 1 str. 9-941 Brucella ceti TE28753-12 Large Cluster (LC) Brucella pinnipedialis B2/94 Brucella microti CCM 4915 Brucella abortus A13334 Brucella melitensis bv. 1 str. 16M LC with putatively pseudogenized genes Brucella ceti TE10759-12 Ochrobactrum anthropi ATCC 49188 Brucella canis HSK A52141 Brucella canis ATCC-23365 LC with bacterial virus genes Brucella suis 1330 ++ [ ] Brucella suis VBI22 Brucella suis ATCC 23445 Brucella ovis ATCC 25840 Bartonella grahamii as4aup LC with putatively pseudogenized and bacterial virus genes Bartonella tribocorum CIP 105476 Bartonella vinsonii subsp. berkhoffii str. Winnie Bartonella henselae str. Houston-1 Bartonella australis Aust/NH1 LC that overlaps with predicted prophage Bartonella bacilliformis KC583 Bartonella quintana str. Toulouse Bartonella quintana RM-11 Bartonella clarridgeiae 73 Mesorhizobium ciceri biovar biserrulae WSM1271 LC that overlaps with predicted prophage and has bacterial virus genes Mesorhizobium loti MAFF303099 Mesorhizobium australicum WSM2073 Mesorhizobium opportunistum WSM2075 Chelativorans sp. BNC1 LC that overlaps with predicted prophage and has putatively pseudogenized genes Sinorhizobium meliloti 2011 Sinorhizobium meliloti Rm41 Sinorhizobium meliloti GR4 Sinorhizobium meliloti SM11 Sinorhizobium meliloti BL225C LC that overlaps with predicted prophage, and has putatively pseudogenized and bacterial virus genes Sinorhizobium meliloti AK83 Sinorhizobium meliloti 1021 Sinorhizobium medicae WSM419 Sinorhizobium fredii USDA 257 Small Cluster (SC) Sinorhizobium fredii NGR234 Rhizobium leguminosarum bv. trifolii WSM1325 Rhizobium leguminosarum bv. viciae 3841* Rhizobium leguminosarum bv. trifolii WSM2304* Rhizobium etli bv. mimosae str. Mim1* SC with putatively pseudogenized genes Rhizobium etli CFN 42 Rhizobium etli CIAT 652 Rhizobium tropici CIAT 899 Rhizobiales Agrobacterium radiobacter K84 SC with bacterial virus genes Agrobacterium vitis S4 Agrobacterium sp. H13-3 Agrobacterium fabrum str. C58 Rhizobium sp. IRBG74 Candidatus Libe ribacter asiaticus str. gxpsy SC with putatively pseudogenized and bacterial virus genes Candidatus Libe ribacter asiaticus str. psy62 Candidatus Liberibacter solanacearum CLsoZC1 Candidatus Libe ribacter americanus str. Sao Paulo Liberibacter crescens BT1 SC within putative prophage region Pelagibacterium halotolerans B2 [Polymorphum gilvum SL003B-26A1] [Pseudovibrio sp. FOBEG1] Bradyrhizobium oligotrophicum S58 Bradyrhizobium sp. BTAi1 SC that overlaps with predicted prophage and has bacterial virus genes Bradyrhizobium sp. ORS 278 Bradyrhizobium sp. S23321 Bradyrhizobium japonicum USDA 6 Bradyrhizobium diazoefficiens USDA 110 SC that overlaps with predicted prophage, and has putatively pseudogenized and bacterial virus genes Nitrobacter hamburgensis X14 Nitrobacter winogradskyi Nb-255 Rhodopseudomonas palustris BisB18 Rhodopseudomonas palustris BisA53 Rhodopseudomonas palustris BisB5 Rhodopseudomonas palustris TIE-1 Rhodopseudomonas palustris DX-1 Rhodopseudomonas palustris HaA2 Oligotropha carboxidovorans OM4 Oligotropha carboxidovorans OM5 ++ [ ] Xanthobacter autotrophicus Py2 Azorhizobium caulinodans ORS 571 Starkeya novella DSM 506 Methylobacterium extorquens AM1 Methylobacterium extorquens DM4 Methylobacterium extorquens CM4 Methylobacterium extorquens PA1 Methylobacterium populi BJ001 Methylobacterium radiotolerans JCM 2831 Methylobacterium nodulans ORS 2060 Methylobacterium sp. 4-46 Beijerinckia indica subsp. indica ATCC 9039 Methylocella silvestris BL2 Methylocystis sp. SC2 Hyphomicrobium denitrificans ATCC 51888 Hyphomicrobium denitrificans 1NES1 Hyphomicrobium sp. MC1 Hyphomicrobium nitrativorans NL23 Rhodomicrobium vannielii ATCC 17100 Parvibaculum lavamentivorans DS1 Phaeobacter inhibens DSM 17395 Phaeobacter gallaeciensis 2.10 Phaeobacter gallaeciensis DSM 26640 Ruegeria sp. TM1040 Leisingera methylohalidivorans DSM 14336 Ruegeria pomeroyi DSS-3 Roseobacter denitrificans OCh 114 Roseobacter litoralis Och 149 Octadecabacter arcticus 238 Octadecabacter antarcticus 307 Dinoroseobacter shibae DFL 12 DSM 16493 Rhodobacterales I Jannaschia sp. CCS1 Rhodobacter sphaeroides KD131 Rhodobacter sphaeroides 2.4.1 Rhodobacter sphaeroides ATCC 17029 Rhodobacter sphaeroides ATCC 17025 Paracoccus denitrificans PD1222 Paracoccus aminophilus JCM 7686 Rhodobacter capsulatus SB1003 (RcGTA) Ketogulonicigenium vulgare WSH-001 Ketogulonicigenium vulgare Y25 Caulobacter crescentus NA1000 Caulobacter crescentus CB15 Caulobacter segnis ATCC 21756 Caulobacter sp. K31 Caulobacterales Phenylobacterium zucineum HLK1 Brevundimonas subvibrioides ATCC 15264 Asticcacaulis excentricus CB 48 [Hyphomonas neptunium ATCC 15444] [Hirschia baltica ATCC 49814] Rhodobacterales II [Maricaulis maris MCS10] Parvularcula bermudensis HTCC2503 Parvularculales Zymomonas mobilis subsp. mobilis ATCC 10988* Zymomonas mobilis subsp-mobilis-str-CP4 = NRRL B-14023 Zymomonas mobilis subsp. mobilis NCIMB 11163* Zymomonas mobilis subsp. mobilis ZM4 ATCC 31821* Zymomonas mobilis subsp. mobilis ATCC 29191* Zymomonas mobilis subsp. pomaceae ATCC 29192* Sphingomonas sp. MM-1 Sphingomonas wittichii RW1* Sphingomonadales Novosphingobium sp PP1Y Novosphingobium aromaticivorans DSM-12444 Erythrobacter litoralis HTCC2594 Sphingopyxis alaskensis RB2256 Sphingobium chlorophenolicum L1 Sphingobium japonicum UT26S Sphingobium sp SYK6 Tistrella mobilis KA081020-065 Acetobacter pasteurianus IFO-3283-01-42C Acetobacter pasteurianus IFO-3283-26 Acetobacter pasteurianus IFO 3283-22 Acetobacter pasteurianus 386B Acetobacter pasteurianus IFO 3283-07 Acetobacter pasteurianus IFO 3283-12 Acetobacter pasteurianus IFO 3283-32 Acetobacter pasteurianus IFO-3283-03 Acetobacter pasteurianus IFO-3283-01 Gluconacetobacter diazotrophicus PAl-5 ++ Gluconacetobacter xylinus NBRC 3288 Gluconobacter oxydans H24 Gluconobacter oxydans 621H Granulibacter bethesdensis CGDNIH1* Acidiphilium cryptum JF-5 Rhodospirillales Acidiphilium multivorum AIU301 Azospirillum lipoferum 4B Azospirillum sp. B510 Azospirillum brasilense Sp245 Rhodospirillum centenum SW [Micavibrio aeruginosavorus ARL13] [Micavibrio aeruginosavorus EPB] Rhodospirillum rubrum F11* Rhodospirillum rubrum ATCC 11170* Rhodospirillum photometricum DSM-122 Magnetospirillum magneticum
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