Table S7: Percentage of significant clusters in which all genes share the same orientation Group 1: Acidobacteria Bacteria Percentage Solibacter usitatus Ellin6076 96.0% Subtotal 96.0% Group 2: Actinobacteria Bacteria Percentage Corynebacterium diphtheriae NCTC 13129 75.0% Corynebacterium efficiens YS-314 88.2% Corynebacterium glutamicum ATCC 13032 93.8% Corynebacterium jeikeium K411 92.3% Mycobacterium sp. KMS 75.0% Mycobacterium sp. MCS 77.4% Mycobacterium avium 104 91.7% Mycobacterium avium subsp. paratuberculosis K-10 81.5% Mycobacterium bovis AF2122/97 82.1% Mycobacterium bovis BCG str. Pasteur 1173P2 82.1% Mycobacterium tuberculosis CDC1551 78.6% Mycobacterium tuberculosis H37Rv 78.6% Mycobacterium leprae TN 94.4% Mycobacterium smegmatis str. MC2 155 83.3% Mycobacterium ulcerans Agy99 87.0% Mycobacterium vanbaalenii PYR-1 73.5% Nocardia farcinica IFM 10152 75.9% Rhodococcus sp. RHA1 72.4% Acidothermus cellulolyticus 11B 96.2% Frankia sp. CcI3 91.7% Frankia alni ACN14a 82.8% Tropheryma whipplei str. Twist 76.9% Tropheryma whipplei TW08/27 76.9% Leifsonia xyli subsp. xyli str. CTCB07 90.9% Arthrobacter sp. FB24 81.8% Arthrobacter aurescens TC1 77.8% Nocardioides sp. JS614 81.5% Propionibacterium acnes KPA171202 95.5% Streptomyces avermitilis MA-4680 78.6% Streptomyces coelicolor A3(2) 95.2% Thermobifida fusca YX 95.2% Bifidobacterium adolescentis ATCC 15703 100.0% Bifidobacterium longum NCC2705 90.9% Rubrobacter xylanophilus DSM 9941 86.2% Subtotal 83.6% Group 3: Alphaproteobacteria Bacteria Percentage Caulobacter crescentus CB15 93.1% Bartonella bacilliformis KC583 95.8% Bartonella henselae str. Houston-1 95.7% Bartonella quintana str. Toulouse 95.7% Bradyrhizobium japonicum USDA 110 71.4% Nitrobacter hamburgensis X14 80.0% Nitrobacter winogradskyi Nb-255 84.8% Rhodopseudomonas palustris BisA53 89.2% Rhodopseudomonas palustris BisB18 73.7% Rhodopseudomonas palustris BisB5 84.2% Rhodopseudomonas palustris CGA009 78.0% Rhodopseudomonas palustris HaA2 79.4% Brucella abortus biovar 1 str. 9-941 82.1% Brucella melitensis 16M 83.9% Brucella melitensis biovar Abortus 2308 82.8% Brucella suis 1330 83.3% Mesorhizobium sp. BNC1 83.3% Mesorhizobium loti MAFF303099 82.4% Agrobacterium tumefaciens str. C58 82.8% Rhizobium etli CFN 42 76.7% Rhizobium leguminosarum bv. viciae 3841 81.8% Sinorhizobium meliloti 1021 75.9% Hyphomonas neptunium ATCC 15444 93.5% Maricaulis maris MCS10 93.5% Jannaschia sp. CCS1 75.0% Paracoccus denitrificans PD1222 88.2% Rhodobacter sphaeroides 2.4.1 86.7% Roseobacter denitrificans OCh 114 92.6% Silicibacter sp. TM1040 84.0% Silicibacter pomeroyi DSS-3 67.9% Gluconobacter oxydans 621H 90.9% Granulibacter bethesdensis CGDNIH1 95.2% Magnetospirillum magneticum AMB-1 78.9% Rhodospirillum rubrum ATCC 11170 93.5% Anaplasma phagocytophilum HZ 100.0% Anaplasma marginale str. St. Maries 100.0% Ehrlichia canis str. Jake 100.0% Ehrlichia chaffeensis str. Arkansas 100.0% Ehrlichia ruminantium str. Gardel 85.7% Ehrlichia ruminantium str. Welgevonden 85.7% Neorickettsia sennetsu str. Miyayama 87.5% Rickettsia conorii str. Malish 7 90.0% Rickettsia felis URRWXCal2 90.9% Rickettsia prowazekii str. Madrid E 80.0% Rickettsia typhi str. Wilmington 100.0% Rickettsia bellii RML369-C 88.9% Wolbachia endosymbiont strain TRS of Brugia malayi 100.0% Wolbachia endosymbiont of Drosophila melanogaster 100.0% Erythrobacter litoralis HTCC2594 91.3% Novosphingobium aromaticivorans DSM 12444 95.8% Sphingopyxis alaskensis RB2256 81.5% Zymomonas mobilis subsp. mobilis ZM4 100.0% Subtotal 85.2% Group 4: Betaproteobacteria Bacteria Percentage Bordetella bronchiseptica RB50 87.5% Bordetella parapertussis 12822 87.2% Bordetella pertussis Tohama I 91.7% Burkholderia sp. 383 90.0% Burkholderia cenocepacia AU 1054 93.9% Burkholderia cenocepacia HI2424 94.0% Burkholderia cepacia AMMD 96.7% Burkholderia mallei ATCC 23344 93.8% Burkholderia mallei SAVP1 94.2% Burkholderia pseudomallei 1710b 94.6% Burkholderia pseudomallei K96243 93.3% Burkholderia thailandensis E264 92.4% Burkholderia xenovorans LB400 82.4% Ralstonia eutropha H16 86.2% Ralstonia eutropha JMP134 82.5% Ralstonia metallidurans CH34 89.2% Ralstonia solanacearum GMI1000 94.4% Acidovorax sp. JS42 94.9% Acidovorax avenae subsp. citrulli AAC00-1 100.0% Polaromonas sp. JS666 85.3% Polaromonas naphthalenivorans CJ2 82.5% Rhodoferax ferrireducens T118 85.7% Verminephrobacter eiseniae EF01-2 83.3% Thiobacillus denitrificans ATCC 25259 95.1% Methylobacillus flagellatus KT 82.1% Chromobacterium violaceum ATCC 12472 89.4% Neisseria gonorrhoeae FA 1090 95.2% Neisseria meningitidis FAM18 90.9% Neisseria meningitidis MC58 90.9% Neisseria meningitidis Z2491 90.9% Nitrosomonas europaea ATCC 19718 100.0% Nitrosomonas eutropha C91 97.0% Nitrosospira multiformis ATCC 25196 100.0% Azoarcus sp. BH72 97.7% Azoarcus sp. EbN1 94.1% Dechloromonas aromatica RCB 95.5% Subtotal 91.2% Group 5: Deltaproteobacteria Bacteria Percentage Bdellovibrio bacteriovorus HD100 100.0% Desulfotalea psychrophila LSv54 90.0% Desulfovibrio desulfuricans G20 88.0% Desulfovibrio vulgaris subsp. vulgaris DP4 96.3% Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough 96.3% Lawsonia intracellularis PHE/MN1-00 92.9% Geobacter metallireducens GS-15 83.3% Geobacter sulfurreducens PCA 93.1% Pelobacter carbinolicus DSM 2380 100.0% Pelobacter propionicus DSM 2379 95.8% Anaeromyxobacter dehalogenans 2CP-C 78.6% Myxococcus xanthus DK 1622 74.3% Syntrophus aciditrophicus SB 92.6% Syntrophobacter fumaroxidans MPOB 92.9% Subtotal 90.2% Group 6: Epsilonproteobacteria Bacteria Percentage Campylobacter fetus subsp. fetus 82-40 80.0% Campylobacter jejuni RM1221 100.0% Campylobacter jejuni subsp. jejuni 81-176 90.5% Campylobacter jejuni subsp. jejuni NCTC 11168 100.0% Helicobacter acinonychis str. Sheeba 100.0% Helicobacter hepaticus ATCC 51449 100.0% Helicobacter pylori 26695 100.0% Helicobacter pylori HPAG1 100.0% Helicobacter pylori J99 100.0% Wolinella succinogenes DSM 1740 81.2% Thiomicrospira denitrificans ATCC 33889 92.9% Subtotal 94.9% Group 7: Gammaproteobacteria Bacteria Percentage Aeromonas hydrophila subsp. hydrophila ATCC 7966 90.0% Marinobacter aquaeolei VT8 95.9% Saccharophagus degradans 2-40 95.2% Colwellia psychrerythraea 34H 90.6% Idiomarina loihiensis L2TR 100.0% Pseudoalteromonas atlantica T6c 95.9% Pseudoalteromonas haloplanktis TAC125 95.8% Psychromonas ingrahamii 37 92.6% Shewanella sp. ANA-3 96.2% Shewanella sp. MR-4 96.6% Shewanella sp. MR-7 94.8% Shewanella sp. W3-18-1 96.6% Shewanella amazonensis SB2B 93.0% Shewanella denitrificans OS217 94.0% Shewanella frigidimarina NCIMB 400 92.6% Shewanella oneidensis MR-1 94.9% Nitrosococcus oceani ATCC 19707 94.1% Alkalilimnicola ehrlichei MLHE-1 92.7% Halorhodospira halophila SL1 86.5% Buchnera aphidicola str. APS (Acyrthosiphon pisum) 95.5% Buchnera aphidicola str. Bp (Baizongia pistaciae) 95.8% Buchnera aphidicola str. Cc (Cinara cedri) 100.0% Buchnera aphidicola str. Sg (Schizaphis graminum) 100.0% Candidatus Blochmannia floridanus 100.0% Candidatus Blochmannia pennsylvanicus str. BPEN 100.0% Escherichia coli 536 90.3% Escherichia coli APEC O1 95.5% Escherichia coli CFT073 94.6% Escherichia coli O157:H7 EDL933 98.3% Escherichia coli O157:H7 str. Sakai 95.7% Escherichia coli UTI89 92.9% Escherichia coli W3110 96.7% Erwinia carotovora subsp. atroseptica SCRI1043 91.9% Photorhabdus luminescens subsp. laumondii TTO1 95.0% Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 95.0% Salmonella enterica subsp. enterica serovar Typhi str. CT18 94.2% Salmonella enterica subsp. enterica serovar Typhi Ty2 94.2% Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 94.1% Salmonella typhimurium LT2 97.2% Shigella boydii Sb227 93.8% Shigella dysenteriae Sd197 96.6% Shigella flexneri 2a str. 2457T 96.0% Shigella flexneri 2a str. 301 95.0% Shigella flexneri 5 str. 8401 96.0% Shigella sonnei Ss046 92.6% Sodalis glossinidius str. 'morsitans' 100.0% Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis 100.0% Yersinia pestis Antiqua 97.3% Yersinia pestis biovar Microtus str. 91001 98.6% Yersinia pestis CO92 98.6% Yersinia pestis KIM 97.3% Yersinia pestis Nepal516 98.6% Yersinia pseudotuberculosis IP 32953 97.3% Coxiella burnetii RSA 493 92.9% Legionella pneumophila str. Lens 100.0% Legionella pneumophila str. Paris 100.0% Legionella pneumophila subsp. pneumophila str. Philadelphia 1 100.0% Methylococcus capsulatus str. Bath 93.5% Alcanivorax borkumensis SK2 91.9% Hahella chejuensis KCTC 2396 94.7% Chromohalobacter salexigens DSM 3043 93.8% Haemophilus ducreyi 35000HP 96.4% Haemophilus influenzae 86-028NP 82.1% Haemophilus influenzae Rd KW20 84.6% Haemophilus somnus 129PT 95.2% Mannheimia succiniciproducens MBEL55E 90.0% Pasteurella multocida subsp. multocida str. Pm70 95.2% Acinetobacter sp. ADP1 85.3% Psychrobacter arcticus 273-4 97.0% Psychrobacter cryohalolentis K5 91.2% Pseudomonas aeruginosa PAO1 96.4% Pseudomonas aeruginosa UCBPP-PA14 98.1% Pseudomonas fluorescens Pf-5 98.0% Pseudomonas fluorescens PfO-1 90.7% Pseudomonas putida KT2440 96.2% Pseudomonas syringae pv. phaseolicola 1448A 96.1% Pseudomonas syringae pv. tomato str. DC3000 88.7% Pseudomonas syringae pv. syringae B728a 85.7% Pseudomonas entomophila L48 96.6% Francisella tularensis subsp. holarctica 100.0% Francisella tularensis subsp. holarctica OSU18 100.0% Francisella tularensis subsp. novicida U112 100.0% Francisella tularensis subsp. tularensis FSC 198 95.0% Francisella tularensis subsp. tularensis SCHU S4 95.0% Thiomicrospira crunogena XCL-2 100.0% Photobacterium profundum SS9 90.4% Vibrio cholerae O1 biovar eltor str. N16961 94.8% Vibrio fischeri ES114 91.9% Vibrio parahaemolyticus RIMD 2210633 92.6% Vibrio vulnificus CMCP6 91.3% Vibrio vulnificus YJ016 90.4% Xanthomonas axonopodis pv. citri str. 306 97.4% Xanthomonas campestris pv. campestris str. 8004 94.4% Xanthomonas campestris pv. campestris str. ATCC 33913 94.3% Xanthomonas campestris pv. vesicatoria str. 85-10 97.1% Xanthomonas oryzae pv. oryzae MAFF 311018 97.3% Xylella fastidiosa 9a5c 100.0% Xylella fastidiosa Temecula1 100.0% Subtotal 94.8% Group 8: Aquificae Bacteria Percentage Aquifex aeolicus VF5 100.0% Subtotal 100.0% Group 9: Bacteroidetes/Chlorobi Bacteria Percentage Bacteroides fragilis NCTC 9343 95.0% Bacteroides fragilis YCH46 100.0% Bacteroides thetaiotaomicron VPI-5482 100.0% Porphyromonas gingivalis W83 100.0% Gramella forsetii KT0803 100.0% Cytophaga hutchinsonii ATCC 33406 95.0% Chlorobium tepidum TLS 100.0% Chlorobium chlorochromatii CaD3 94.1% Chlorobium phaeobacteroides DSM 266 100.0% Pelodictyon luteolum DSM 273 100.0% Subtotal 98.4% Group 10: Chlamydiae/Verrucomicrobia Bacteria Percentage Chlamydia muridarum Nigg 88.9% Chlamydia trachomatis A/HAR-13 90.9% Chlamydia trachomatis D/UW-3/CX 90.9% Chlamydophila abortus S26/3 90.0% Chlamydophila caviae GPIC 91.7% Chlamydophila felis Fe/C-56 91.7% Chlamydophila pneumoniae AR39 100.0% Chlamydophila pneumoniae CWL029 100.0% Chlamydophila pneumoniae J138 100.0% Chlamydophila pneumoniae TW-183 100.0% Candidatus Protochlamydia amoebophila UWE25 100.0% Subtotal 95.2% Group 11: Chloroflexi Bacteria Percentage Dehalococcoides sp. CBDB1 84.2% Dehalococcoides ethenogenes 195 93.8% Subtotal 88.6% Group 12: Cyanobacteria Bacteria Percentage Gloeobacter violaceus PCC 7421 83.3% Synechococcus elongatus PCC 6301 91.7% Synechococcus elongatus PCC 7942 91.7% Synechococcus sp. CC9311 66.7% Synechococcus sp. CC9605 70.0% Synechococcus sp. CC9902 70.0% Synechococcus sp. JA-2-3B'a(2-13) 100.0% Synechococcus sp. JA-3-3Ab 90.9% Synechococcus sp. WH 8102 70.0% Synechocystis sp. PCC 6803 100.0% Thermosynechococcus elongatus BP-1 100.0% Anabaena variabilis ATCC 29413 87.5% Nostoc sp. PCC 7120 89.5% Trichodesmium erythraeum IMS101 92.9% Prochlorococcus marinus str. MIT 9312 66.7% Prochlorococcus marinus str. MIT 9313 70.0% Prochlorococcus marinus str. NATL2A 77.8% Prochlorococcus marinus subsp. marinus str. CCMP1375 75.0% Prochlorococcus marinus subsp. pastoris str. CCMP1986 60.0% Subtotal 82.6% Group 13: Deinococcus-Thermus Bacteria Percentage Deinococcus geothermalis DSM 11300 100.0% Deinococcus radiodurans R1 93.8% Thermus thermophilus HB27 75.0% Thermus thermophilus HB8 81.2% Subtotal 87.1% Group 14: Firmicutes Bacteria Percentage Bacillus anthracis str. 'Ames Ancestor' 91.7% Bacillus anthracis str. Ames 91.7% Bacillus anthracis str. Sterne 91.7% Bacillus cereus ATCC 10987 91.4% Bacillus cereus ATCC 14579 94.7% Bacillus cereus E33L 91.7% Bacillus thuringiensis serovar konkukian str. 97-27 91.7% Bacillus thuringiensis str. Al Hakam 91.9% Bacillus clausii KSM-K16 81.8% Bacillus halodurans C-125 82.8% Bacillus licheniformis ATCC 14580 96.6% Bacillus subtilis subsp. subtilis str. 168 84.2% Geobacillus kaustophilus HTA426 100.0% Oceanobacillus iheyensis HTE831 93.1% Listeria innocua Clip11262 95.5% Listeria monocytogenes EGD-e 90.5% Listeria monocytogenes str. 4b F2365 95.2% Listeria welshimeri serovar 6b str. SLCC5334 95.0% Staphylococcus aureus RF122 92.0% Staphylococcus aureus subsp. aureus COL 92.0% Staphylococcus aureus subsp. aureus MRSA252 91.7% Staphylococcus aureus subsp. aureus MSSA476 92.0% Staphylococcus aureus subsp. aureus Mu50 92.0% Staphylococcus aureus subsp. aureus MW2 92.0% Staphylococcus aureus subsp. aureus N315 92.0% Staphylococcus aureus subsp. aureus NCTC 8325 91.7% Staphylococcus aureus subsp. aureus USA300 92.0% Staphylococcus epidermidis ATCC 12228 87.0% Staphylococcus epidermidis RP62A 87.5% Staphylococcus haemolyticus JCSC1435 86.4% Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 85.7% Enterococcus faecalis V583 100.0% Lactobacillus acidophilus NCFM 75.0% Lactobacillus brevis ATCC 367 100.0% Lactobacillus casei ATCC 334 88.2% Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 100.0% Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 100.0% Lactobacillus gasseri ATCC 33323 87.5% Lactobacillus johnsonii NCC 533 100.0% Lactobacillus plantarum WCFS1 95.0% Lactobacillus sakei subsp. sakei 23K 100.0% Lactobacillus salivarius subsp. salivarius UCC118 100.0% Pediococcus pentosaceus ATCC 25745 100.0% Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 70.8% Oenococcus oeni PSU-1 87.5% Lactococcus lactis subsp. cremoris SK11 100.0% Lactococcus lactis subsp. lactis Il1403 100.0% Streptococcus agalactiae 2603V/R 100.0% Streptococcus agalactiae A909 90.9% Streptococcus agalactiae NEM316 87.5% Streptococcus mutans UA159 94.4% Streptococcus pneumoniae D39 100.0% Streptococcus pneumoniae R6 100.0% Streptococcus pneumoniae TIGR4 100.0% Streptococcus pyogenes M1 GAS 100.0% Streptococcus pyogenes MGAS10270 100.0% Streptococcus pyogenes MGAS10394 100.0% Streptococcus pyogenes MGAS10750 100.0% Streptococcus pyogenes MGAS2096 100.0% Streptococcus pyogenes MGAS315 100.0% Streptococcus pyogenes MGAS5005 100.0% Streptococcus pyogenes MGAS6180 100.0% Streptococcus pyogenes MGAS8232 100.0% Streptococcus pyogenes MGAS9429 100.0% Streptococcus pyogenes SSI-1 100.0% Streptococcus thermophilus CNRZ1066 100.0% Streptococcus thermophilus LMD-9 100.0% Streptococcus thermophilus LMG 18311 100.0% Clostridium acetobutylicum ATCC 824 73.1% Clostridium novyi NT 94.4% Clostridium perfringens ATCC 13124 95.2% Clostridium perfringens SM101 100.0% Clostridium perfringens str. 13 94.4% Clostridium tetani E88 89.5% Carboxydothermus hydrogenoformans Z-2901 100.0% Desulfitobacterium hafniense Y51 91.2% Syntrophomonas wolfei subsp. wolfei str. Goettingen 100.0% Moorella thermoacetica ATCC 39073 100.0% Thermoanaerobacter tengcongensis MB4 100.0% Aster yellows witches'-broom phytoplasma AYWB 100.0% Onion yellows phytoplasma OY-M 100.0% Mesoplasma florum L1 100.0% Mycoplasma capricolum subsp. capricolum ATCC 27343 87.5% Mycoplasma gallisepticum R 100.0% Mycoplasma genitalium G37 100.0% Mycoplasma hyopneumoniae 232 100.0% Mycoplasma hyopneumoniae 7448 80.0% Mycoplasma hyopneumoniae J 83.3% Mycoplasma mobile 163K 100.0% Mycoplasma mycoides subsp. mycoides SC str. PG1 87.5% Mycoplasma penetrans HF-2 100.0% Mycoplasma pneumoniae M129 80.0% Mycoplasma pulmonis UAB CTIP 100.0% Mycoplasma synoviae 53 75.0% Ureaplasma parvum serovar 3 str. ATCC 700970 100.0% Subtotal 93.0% Group 15: Fusobacteria Bacteria Percentage Fusobacterium nucleatum subsp. nucleatum ATCC 25586 85.7% Subtotal 85.7% Group 16: Planctomycetes Bacteria Percentage Rhodopirellula baltica SH 1 100.0% Subtotal 100.0% Group 17: Spirochaetes Bacteria Percentage Leptospira borgpetersenii serovar Hardjo-bovis JB197 92.9% Leptospira borgpetersenii serovar Hardjo-bovis L550 92.9% Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 93.3% Leptospira interrogans serovar Lai str. 56601 93.3% Borrelia afzelii PKo 100.0% Borrelia burgdorferi B31 100.0% Borrelia garinii PBi 100.0% Treponema denticola ATCC 35405 76.9% Treponema pallidum subsp. pallidum str. Nichols 100.0% Subtotal 93.3% Group 18: Thermotogae Bacteria Percentage Thermotoga maritima MSB8 94.7% Subtotal 94.7%