The chromatin insulator CTCF and the emergence of metazoan diversity Peter Heger, Birger Marin, Marek Bartkuhn, Einhard Schierenberg, Thomas Wiehe Supporting Information 1 Pleurobrachia pileus, Ctenophora, FQ006515 Pleurobrachia pileus, Ctenophora, CU423733 Nematostella vectensis, Cnidaria, XP_001634899 Nematostella vectensis, Cnidaria, XP_001640902 Hydra magnipapillata, Cnidaria, XP_002167862 Nematostella vectensis, Cnidaria, XP_001634190 Hydra magnipapillata, Cnidaria, XP_002162913 Nematostella vectensis, Cnidaria, XP_001638437 Pleurobrachia pileus, Ctenophora, FP991204 Nematostella vectensis, Cnidaria, jgi_23405|gw.130.55.1 Nematostella vectensis, Cnidaria, XP_001633145 100/1.00 Nematostella vectensis, Cnidaria, jgi_34044|gw.27.97.1 Nematostella vectensis, Cnidaria, XP_001627859 Nematostella vectensis, Cnidaria, XP_001627106 Nematostella vectensis, Cnidaria, XP_001630930 Nematostella vectensis, Cnidaria, XP_001637077 Nematostella vectensis, Cnidaria, XP_001638320 Nematostella vectensis, Cnidaria, XP_001639816 Pleurobrachia pileus, Ctenophora, CU419619 Pleurobrachia pileus, Ctenophora, CU421239 Hydra magnipapillata, Cnidaria, XP_002165457 Nematostella vectensis, Cnidaria, jgi_32594|gw.18.48.1 Nematostella vectensis, Cnidaria, XP_001628755 Nematostella vectensis, Cnidaria, XP_001623148 100/1.00 Hydra magnipapillata, Cnidaria, XP_002156009 Nematostella vectensis, Cnidaria, XP_001635170 Nematostella vectensis, Cnidaria, XP_001640317 98/1.00 Hydra magnipapillata, Cnidaria, XP_002164347 Nematostella vectensis, Cnidaria, XP_001627411 Trichoplax adhaerens, Placozoa, XP_002107781 62/- Nematostella vectensis, Cnidaria, XP_001638691 Trichoplax adhaerens, Placozoa, XP_002115480 Nematostella vectensis, Cnidaria, XP_001630609 Nematostella vectensis, Cnidaria, XP_001625440 84/0.97 Pleurobrachia pileus, Ctenophora, FP996443 Pleurobrachia pileus, Ctenophora, CU419106 Nematostella vectensis, Cnidaria, jgi_1034|gw.318.8.1 Nematostella vectensis, Cnidaria, jgi_31930|gw.14.46.1 Nematostella vectensis, Cnidaria, jgi_99869|e gw.54.13.1 Nematostella vectensis, Cnidaria, jgi_13117|gw.115.17.1 Nematostella vectensis, Cnidaria, jgi_21241|gw.147.19.1b Nematostella vectensis, Cnidaria, jgi_21241|gw.147.19.1a Nematostella vectensis, Cnidaria, XP_001637546 55/0.99 Nematostella vectensis, Cnidaria, XP_001627149 73/0.87 61/1.00 Nematostella vectensis, Cnidaria, jgi_23524|gw.48.32.1 Nematostella vectensis, Cnidaria, XP_001632184 Nematostella vectensis, Cnidaria, jgi_33793|gw.35.78.1 Nematostella vectensis, Cnidaria, jgi_32220|gw.10.54.1 Nematostella vectensis, Cnidaria, XP_001627957 Nematostella vectensis, Cnidaria, jgi_192|gw.361.3.1b Nematostella vectensis, Cnidaria, jgi_1904|gw.2641.1.1 Nematostella vectensis, Cnidaria, jgi_10533|gw.1453.3.1b 65/0.86 Nematostella vectensis, Cnidaria, jgi_135736|e gw.361.1.1b Nematostella vectensis, Cnidaria, jgi_966|gw.2770.1.1 Nematostella vectensis, Cnidaria, XP_001618979 Nematostella vectensis, Cnidaria, XP_001623938 Nematostella vectensis, Cnidaria, jgi_22037|gw.86.101.1 Nematostella vectensis, Cnidaria, XP_001622248 Nematostella vectensis, Cnidaria, jgi_107|gw.375.1.1 Nematostella vectensis, Cnidaria, jgi_192|gw.361.3.1a Nematostella vectensis, Cnidaria, jgi_22123|gw.105.28.1a Nematostella vectensis, Cnidaria, jgi_21470|gw.105.24.1b Nematostella vectensis, Cnidaria, jgi_10533|gw.1453.3.1a Nematostella vectensis, Cnidaria, jgi_22123|gw.105.28.1b Nematostella vectensis, Cnidaria, jgi_21470|gw.105.24.1a 54/0.96 Nematostella vectensis, Cnidaria, jgi_20972|gw.63.26.1b Nematostella vectensis, Cnidaria, jgi_20972|gw.63.26.1a Nematostella vectensis, Cnidaria, XP_001624941 Nematostella vectensis, Cnidaria, jgi_22113|gw.136.23.1 89/1.00 Nematostella vectensis, Cnidaria, jgi_20980|gw.63.27.1a Nematostella vectensis, Cnidaria, jgi_20980|gw.63.27.1b -/1.00 Nematostella vectensis, Cnidaria, jgi_135736|e gw.361.1.1a Nematostella vectensis, Cnidaria, jgi_3275|gw.4450.2.1 Nematostella vectensis, Cnidaria, jgi_135772|e gw.361.16.1b Nematostella vectensis, Cnidaria, XP_001633554 Nematostella vectensis, Cnidaria, XP_001634723 Nematostella vectensis, Cnidaria, XP_001629021 Nematostella vectensis, Cnidaria, XP_001629912 Nematostella vectensis, Cnidaria, jgi_101176|e gw.60.8.1 Nematostella vectensis, Cnidaria, XP_001630482 Nematostella vectensis, Cnidaria, XP_001634081 100/0.91 Amphimedon queenslandica, Porifera, Aqu1.227223 Amphimedon queenslandica, Porifera, Aqu1.227222 Nematostella vectensis, Cnidaria, XP_001626384 Pleurobrachia pileus, Ctenophora, FQ003013 Nematostella vectensis, Cnidaria, jgi_21453|gw.139.32.1 Nematostella vectensis, XP_001635337 Trichoplax adhaerens, Placozoa, XP_002112782 Trichoplax adhaerens, Placozoa, XP_002118240 Pleurobrachia pileus, Ctenophora, CU418523 Trichoplax adhaerens, Placozoa, XP_002113391 Nematostella vectensis, Cnidaria, XP_001633421 Trichoplax adhaerens, Placozoa, jgi_20484|e gw1.2.876.1 99/1.00 Trichoplax adhaerens, Placozoa, XP_002110060 Trichoplax adhaerens, Placozoa, XP_002109514 Nematostella vectensis, Cnidaria, XP_001633558 Hydra magnipapillata, Cnidaria, XP_002164561 Nematostella vectensis, Cnidaria, XP_001628695 Nematostella vectensis, Cnidaria, XP_001638633 Amphimedon queenslandica, Porifera, Aqu1.218884 Nematostella vectensis, Cnidaria, XP_001632099 Nematostella vectensis, Cnidaria, XP_001636147 100/1.00 Saccoglossus kowalevskii, Hemichordata, ACQM01099953 100/1.00 Paracentrotus lividus, Echinodermata, AM584769 Deuterostomia (Echinodermata, Hemichordata) Strongylocentrotus purpuratus, Echinodermata, XM_001182546 Branchiostoma floridae, Cephalochordata, BW735442 100/1.00 Molgula tectiformis, Tunicata, CJ411890 Halocynthia roretzi, Tunicata, DB583237 96/0.88 Ciona intestinalis, Tunicata, NP_001104593 Gasterosteus aculeatus, Vertebrata, Teleostei, DN695373 84/- Hippoglossus hippoglossus, Vertebrata, Teleostei, CF931824 99/1.00 54/0.93 Salmo salar, Vertebrata, Teleostei, EG908850 54/- Oncorhynchus nerka, Vertebrata, Teleostei, EV376598 Pimephales promelas, Vertebrata, Teleostei, GH713274 Danio rerio, Vertebrata, Teleostei, NM_001001844 Deuterostomia (Chordata) Ictalurus punctatus, Vertebrata, Teleostei, FD319623 Bilaterian CTCF-clade Gallus gallus, Vertebrata, Aves, NM_205332 Macropus eugenii, Mammalia, Metatheria, EU527852 92/0.99 Pogona vitticeps, Lepidosauria, Squamata, EU527854 Bos taurus, Mammalia, Ruminantia, NM_001075748 64/0.92 Mus musculus, Mammalia, Rodentia, NM_181322 75/0.81 Homo sapiens, Mammalia, Primates, NM_006565 Ornithorhynchus anatinus, Mammalia, Monotremata, NM_001123357 Petromyzon marinus, Vertebrata, Agnatha, DW022714 Brachionus plicatilis branch reduced by 50 % , Rotifera, FM904670 Protostomia (Lophotrochozoa) Milnesium tardigradum , Tardigrada, GR863778 (Ecdysozoa) 72/1.00 Trichinella spiralis, Nematoda, FM991921 Protostomia Crassostrea virginica, Mollusca, Bivalvia, EH644958 Lottia gigantea, Mollusca, Gastropoda, genomic scaffold 219 Protostomia (Lophotrochozoa) Aplysia californica, Mollusca, Gastropoda, AASC02025622, AASC02025623 Capitella sp., Annelida, Polychaeta, genomic scaffold 915 98/1.00 Hirudo medicinalis, Annelida, Hirudinea, EY489143 Helobdella sp., Annelida, Hirudinea, genomic scaffold 42 Sequence Data: Alvinella pompejana, Annelida, Polychaeta, GO140543 Tetranychus urticae, Arachnida, Acari, GW042583 275 aligned amino acid positions of 57 CTCF proteins Ixodes scapularis, Arachnida, Acari, XP_002413501 Lepeophtheirus salmonis, Crustacea, Copepoda, EY509071 61/1.00 from bilaterians and 105 non-CTCF ZF proteins from: -/0.98 Pediculus humanus corporis, Insecta, Phthiraptera, XP_002431599 Tribolium castaneum, Insecta, Coleoptera, EFA00140 - Trichoplax adhaerens (Placozoa; genome) Apis mellifera, Insecta, Hymenoptera, BI946444, AADG05000405 Nasonia vitripennis, Insecta, Hymenoptera, XP_001606075 Protostomia (Ecdysozoa) - Pleurobrachia pileus (Ctenophora; 51,042 ESTs) Anopheles gambiae, Insecta, Diptera, XP_315558 98/1.00 Aedes aegypti, Insecta, Diptera, AAY15453 - Amphimedon queenslandica (Porifera; genome) 98/1.00 Culex quinquefasciatus, Insecta, Diptera, XP_001850306 65/1.00 Nilaparvata lugens, Insecta, Hemiptera, DB844012 - Nematostella vectensis and Acyrthosiphon pisum, Insecta, Hemiptera, NW_001928160 100/1.00 Drosophila willistoni, Insecta, Diptera, XP_002062418 - Hydra magnipapillata (Cnidaria; genome) Drosophila pseudoobscura, Insecta, Diptera, EAL30192 Drosophila melanogaster, Insecta, Diptera, NP_648109 Tree topology: Drosophila virilis, Insecta, Diptera, XP_002046880 100/1.00 Drosophila grimshavi, Insecta, Diptera, XP_001983788 maximum likelihood (RAxML; model: WAG+Γ) 93/0.99 Bicyclus anynana, Insecta, Lepidoptera, GE734255 Danaus plexippus, Insecta, Lepidoptera, EY263249 Significances at branches: Laupala kohalensis, Insecta, Orthoptera, EH638023 Celuca pugilator, Crustacea, Malacostraca, DW176201 maximum likelihood (bootstrap values >50) / MrBayes Litopenaeus vannamei, Crustacea, Malacostraca, FE077232 Homarus americanus, Crustacea, Malacostraca, EX487114 (posterior probabilities >0.80) 85/1.00 Callinectes sapidus, Crustacea, Malacostraca, CV162031 Daphnia pulex, Crustacea, Branchiopoda, genomic scaffolds 158, 1460 78/0.93 Pleurobrachia pileus, Ctenophora, CU417453 Hydra magnipapillata, Cnidaria, XP_002161321 Hydra magnipapillata 57/- , Cnidaria, XP_002171280 Acyrthosiphon pisum, Insecta, Hemiptera, XP_001947579 79/1.00 100/1.00 Drosophila melanogaster, Insecta, Diptera, NP_477243 90/1.00 Drosophila pseudoobscura, Insecta, Diptera, EDY69939 100/1.00 Tribolium castaneum, Insecta, Coleoptera, XP_973800 Apis mellifera, Insecta, Hymenoptera, XP_392980