S8 Table: List of all eukaryotic organisms. NCBI # assembly_accession RefSeq Ku et al. JGI GenBank Ensembl species_taixid short file_conv # proteins # proteins with hit in other species % proteins with best hit in other species # proteins with more than one hit in same species % proteins with more than one hit in same species Supergroups Sub-Supergroup assembly lvl according to RefSeq Source of nuclear-encoded protein sequences Source of mitochondrial genome sequence/Accession number (downloaded in November 2014) Source of plastid genome sequence/Accession number (downloaded in November 2014) Superkingdom Kingdom Phylum Class Order Family Genus Species Acanthamoeba castellanii str. Neff GCF_000313135.1 + 5755 MAC file_1 14974 10700 71,46 9958 66,50 Mycetozoa Discosea Scaffold http://www.ncbi.nlm.nih.gov/bioproject/193615 NC_001637 - Homo sapiens GCF_000001405.37 + 9606 OHS file_10 109052 105574 96,81 104598 95,92 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia Primates Hominidae Homo Homo sapiens Pochonia chlamydosporia 170 GCF_001653235.2 + 280754 OPC file_100 14204 11400 80,26 7696 54,18 Opisthokonta Fungi Chromosome Eukaryota Fungi Ascomycota Sordariomycetes Hypocreales Clavicipitaceae Pochonia Pochonia chlamydosporia Nothobranchius furzeri GCF_001465895.1 + 105023 ONF file_101 36873 36711 99,56 34287 92,99 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Actinopteri Cyprinodontiformes Nothobranchiidae Nothobranchius Nothobranchius furzeri Schizosaccharomyces pombe GCF_000002945.1 + 4896 OSP file_102 5132 4436 86,44 2229 43,43 Opisthokonta Fungi Chromosome Eukaryota Fungi Ascomycota Schizosaccharomycetes Schizosaccharomycetales Schizosaccharomycetaceae Schizosaccharomyces Schizosaccharomyces pombe Chrysemys picta bellii GCF_000241765.3 + 8479 OCP file_103 42558 42402 99,63 40221 94,51 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata - Testudines Emydidae Chrysemys Chrysemys picta Nannochloropsis gaditana CCMP526 GCF_000240725.1 + 72520 SNG file_104 3554 2575 72,45 1369 38,52 SAR Stramenopiles Scaffold http://www.nannochloropsis.org/ NC_022254 NC_020014 Bombus terrestris GCF_000214255.1 + 30195 OBT file_105 22091 21652 98,01 19292 87,33 Opisthokonta Animalia Chromosome Eukaryota Metazoa Arthropoda Insecta Hymenoptera Apidae Bombus Bombus terrestris Encephalitozoon cuniculi GB-M1 GCF_000091225.1 + 6035 OEC file_106 1996 1928 96,59 598 29,96 Opisthokonta Fungi Chromosome Eukaryota Fungi Microsporidia - - Unikaryonidae Encephalitozoon Encephalitozoon cuniculi Canis lupus familiaris GCF_000002285.3 + 9612 OCL file_107 58774 57860 98,44 56504 96,14 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia Carnivora Canidae Canis Canis lupus Schistosoma mansoni GCF_000237925.1 + 6183 OSM file_108 11713 8337 71,18 6318 53,94 Opisthokonta Animalia Chromosome Eukaryota Metazoa Platyhelminthes Trematoda Strigeidida Schistosomatidae Schistosoma Schistosoma mansoni Saksenaea vasiformis B4078 Sakvas1_GeneCatalog_proteins_20160730.aa.fasta.gz + 1274794 OSV file_109 9387 9152 97,50 6771 72,13 Opisthokonta Fungi Contig JNDT00000000.1 Eukaryota Fungi Mucoromycota Mucorales Saksenaeaceae Saksenaea Saksenaea vasiformis Hesseltinella vesiculosa NRRL 3301 Hesve2finisherSC_GeneCatalog_proteins_20150707.aa.fasta.gz + 101127 OHV file_11 11141 9661 86,72 7162 64,29 Opisthokonta Fungi http://genome.jgi.doe.gov/Hesve2finisherSC Eukaryota Fungi Mucoromycota Mucorales Cunninghamellaceae Hesseltinella Aedes aegypti GCF_002204515.2 + 7159 OAA file_110 28317 27312 96,45 25446 89,86 Opisthokonta Animalia Chromosome Eukaryota Metazoa Arthropoda Insecta Diptera Culicidae Aedes Aedes aegypti Tribolium castaneum GCF_000002335.3 + 7070 OTC file_111 22610 20860 92,26 19458 86,06 Opisthokonta Animalia Chromosome Eukaryota Metazoa Arthropoda Insecta Coleoptera Tenebrionidae Tribolium Tribolium castaneum Cyanophora paradoxa Cyanophora_paradoxa.faa.gz (von Ku et al.) + 2762 ACP file_112 32167 12903 40,11 14160 44,02 Archaeplastida Glaucophyta NC_017836 (mitochondrial, complete genome)/NC_001675 (cyanelle, complete genome) http://cyanophora.rutgers.edu/cyanophora/ NC_017836 NC_001675 Symbiodinium minutum symbB.v1.2.augustus.prot.fa.gz 1202447 SSM file_113 47014 25676 54,61 33711 71,70 SAR Alveolata not in refseq / Genbank Scaffold (GCA_000507305.1) http://marinegenomics.oist.jp/genomes/ - http://marinegenomics.oist.jp/genomes/ Linderina pennispora ATCC 12442 Linpe1_GeneCatalog_proteins_20150915.aa.fasta.gz + 61395 OLP file_114 9351 7672 82,04 4909 52,50 Opisthokonta Fungi http://genome.jgi.doe.gov/Linpe1 Eukaryota Fungi Zoopagomycota Kickxellales Kickxellaceae Linderina Mus musculus GCF_000001635.26 + 10090 OMMU file_115 76226 75287 98,77 74562 97,82 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia Rodentia Muridae Mus Mus musculus Plasmodiophora brassicae Plasmodiophora_brassicae.pbe3.h15.pep.all.fa.gz + 37360 SPB file_116 9727 7223 74,26 5178 53,23 SAR Rhizaria Scaffold http://protists.ensembl.org/Plasmodiophora_brassicae/Info/Index Lichtheimia corymbifera FSU 9682 GCA_000723665.1 + 1263082 OLC file_117 13404 11114 82,92 9979 74,45 Opisthokonta Fungi Scaffold CBTN000000000.1 Eukaryota Fungi Mucoromycota Mucorales Lichtheimiaceae Lichtheimia Lichtheimia corymbifera Ovis aries GCF_000298735.2 + 9940 OOA file_118 43036 42830 99,52 40380 93,83 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia - Bovidae Ovis Ovis aries Coturnix japonica GCF_001577835.1 + 93934 OCJAP file_119 39088 38902 99,52 36949 94,53 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Aves Galliformes Phasianidae Coturnix Coturnix japonica Macaca mulatta GCF_000772875.2 + 9544 OMM file_12 55312 54991 99,42 53038 95,89 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia Primates Cercopithecidae Macaca Macaca mulatta Batrachochytrium dendrobatidis JAM81 GCF_000203795.1 + 109871 OBD file_120 8700 6846 78,69 4498 51,70 Opisthokonta Fungi Scaffold ADAR00000000.1 Eukaryota Fungi Chytridiomycota Chytridiomycetes Rhizophydiales Betrachochytrium Batrachochytrium dendrobatidis Ciona intestinalis GCF_000224145.2 + 7719 OCI file_121 18958 16672 87,94 15476 81,63 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Ascidiacea Enterogona Cionidae Ciona Ciona intestinalis Neurospora crassa OR74A GCF_000182925.2 + 5141 ONC file_122 10812 8996 83,20 5358 49,56 Opisthokonta Fungi Chromosome Eukaryota Fungi Ascomycota Sordariomycetes Sordariales Sordariaceae Neurospora Neurospora crassa Cynoglossus semilaevis GCF_000523025.1 + 244447 OCS file_123 36992 36901 99,75 34560 93,43 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Actinopteri Pleuronectiformes Cynoglossidae Cynoglossus Cynoglossus semilaevis Esox lucius GCF_000721915.3 + 8010 OEL file_124 51357 51212 99,72 49274 95,94 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Actinopteri Esociformes Esocidae Esox Esox lucius Plasmodium chabaudi chabaudi GCF_900002335.2 + 5825 SPC file_125 5158 4843 93,89 1656 32,11 SAR Alveolata Chromosome Eukaryota - Apicomplexa Aconoidasida Haemosporida Plasmodiidae Plasmodium Plasmodium chabaudi Thalassiosira pseudonana CCMP1335 GCF_000149405.2 + 35128 STPS file_126 11673 9425 80,74 6487 55,57 SAR Stramenopiles Chromosome Eukaryota - Bacillariophyta Coscinodiscophyceae Thalassiosirales Thalassiosiraceae Thalassiosira Thalassiosira pseudonana Porphyridium purpureum Porphyridium_purpureum.faa.gz (Ku et al.) + 35688 APPU file_127 8355 6568 78,61 4148 49,65 Archaeplastida Rhodophyceae NC_023133 (chloroplast, complete genome)/ Genbank Contig ( GCA_000397085.1 Porphyridium purpureum) http://cyanophora.rutgers.edu/porphyridium/ - NC_023133 Oreochromis niloticus GCF_001858045.1 + 8128 OON file_128 58087 57576 99,12 56071 96,53 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Actinopteri Cichliformes Cichlidae Oreochromis Oreochromis niloticus Homoloaphlyctis polyrhiza JEL142 v1 Hompol1_GeneCatalog_proteins_20160803.aa.fasta.gz + 166479 OHP file_129 7123 6386 89,65 2918 40,97 Opisthokonta Fungi Scaffold AFSM01000000.1 (Joneson et al. 2011) Eukaryota Fungi Chytridiomycota Chytridiomycetes Rhizophydiales Homolaphlyctis Homolaphlyctis polyrhiza Ectocarpus siliculosus EctsiV2_prot_LATEST.tfa.gz 2880 SES file_13 16361 10880 66,50 8402 51,35 SAR Stramenopiles not in refseq / Genbank Chromosome ( GCA_000310025.1 ASM31002v1) https://bioinformatics.psb.ugent.be/gdb/ectocarpus/ - NC_013498 Phaeodactylum tricornutum CCAP 1055/1 GCF_000150955.2 + 2850 SPT file_130 10408 8874 85,26 5652 54,30 SAR Stramenopiles Chromosome Eukaryota - Bacillariophyta Bacillariophyceae Naviculales Phaeodactylaceae Phaeodactylum Phaeodactylum tricornutum Anopheles gambiae str. PEST GCF_000005575.2 + 7165 OAG file_131 14099 13242 93,92 9714 68,90 Opisthokonta Animalia Chromosome Eukaryota Metazoa Arthropoda Insecta Diptera Culicidae Anopheles Anopheles gambiae Vitrella brassicaformis GCA_001179505.1 + 1169540 SVB file_132 23034 13167 57,16 15868 68,89 SAR Alveolata Scaffold Capsaspora owczarzaki ATCC 30864 GCF_000151315.2 + 192875 OCO file_133 8792 7450 84,74 4850 55,16 Opisthokonta Ichthyosporea Scaffold http://www.broadinstitute.org/annotation/genome/multicellularity_project/ http://www.broadinstitute.org/annotation/genome/multicellularity_project/ - Trichoplax adhaerens GCF_000150275.1 + 10228 OTA file_134 11520 10062 87,34 7251 62,94 Opisthokonta Animalia Scaffold ftp://ftp.jgi-psf.org/pub/JGI_data/Trichoplax_adhaerens_Grell-BS-1999/ NC_008151 - Drosophila pseudoobscura pseudoobscura GCF_000001765.3 + 7237 ODP file_135 23456 22897 97,62 19348 82,49 Opisthokonta Animalia Chromosome Eukaryota Metazoa Arthropoda Insecta Diptera Drosophilidae Drosophila Drosophila pseudoobscura Apis mellifera GCF_000002195.4 + 7460 OAM file_136 22451 21791 97,06 19438 86,58 Opisthokonta Animalia Chromosome Eukaryota Metazoa Arthropoda Insecta Hymenoptera Apidae Apis Apis mellifera Rhizopus delemar RA 99-880 GCA_000149305.1 + 246409 ORD file_137 17459 14496 83,03 13396 76,73 Opisthokonta Fungi Scaffold AACW00000000.2 (Ma et al. 2009) Eukaryota Fungi Mucoromycota Mucorales Rhizopodaceae Rhizopus Rhizopus delemar Nasonia vitripennis GCF_000002325.3 + 7425 ONV file_138 24846 22831 91,89 21813 87,79 Opisthokonta Animalia Chromosome Eukaryota Metazoa Arthropoda Insecta Hymenoptera Pteromalidae Nasonia Nasonia vitripennis Guillardia theta CCMP2712 GCF_000315625.1 + 55529 HGT file_139 24822 14776 59,53 14716 59,29 Hacrobia Cryptophyta Scaffold http://genome.jgi.doe.gov/Guith1/download/ - NC_000926 Orpinomyces sp. C1A Orpsp1_1_GeneCatalog_proteins_20140826.aa.fasta.gz + 1987568 OOC1A file_14 18936 16390 86,55 14898 78,68 Opisthokonta Fungi Contig ASRE00000000.1 (Youssef et al. 2013) Eukaryota Fungi Chytridiomycota Neocallimastigomycetes Neocallimastigales Neocallimastigaceae Pecoramyces Trichomonas vaginalis G3 GCF_000002825.2 + 5722 ETV file_140 59679 18250 30,58 54897 91,99 Excavata Metamonoada Scaffold http://trichdb.org/common/downloads/ - - Xenopus laevis GCF_001663975.1 + 8355 OXL file_141 56667 55989 98,80 55419 97,80 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Amphibia Anura Pipidae Xenopus Xenopus laevis Theileria equi strain WA GCF_000342415.1 + 5872 STE file_142 5329 3990 74,87 2639 49,52 SAR Alveolata Chromosome Eukaryota - Apicomplexa Aconoidasida - Theileriidae Theileria Theileria equi Encephalitozoon romaleae SJ-2008 GCF_000280035.1 + 571949 OER file_143 1831 1825 99,67 392 21,41 Opisthokonta Fungi Chromosome Eukaryota Fungi Microsporidia - - Unikaryonidae Encephalitozoon Encephalitozoon romaleae Cyanidioschyzon merolae strain 10D GCF_000091205.1 + 45157 ACM file_144 4803 3994 83,16 1810 37,68 Archaeplastida Rhodophyceae Complete Genome Eukaryota - - Bangiophyceae Cyanidiales Cyanidiaceae Cyanidioschyzon Cyanidioschyzon merolae Babesia bigemina GCF_000981445.1 + 5866 SBBI file_145 5079 4209 82,87 2290 45,09 SAR Alveolata Chromosome Eukaryota - Apicomplexa Aconoidasida - Babesiidae Babesia Babesia bigemina Sorghum bicolor GCF_000003195.3 + 4558 ASB file_146 39248 37517 95,59 36315 92,53 Archaeplastida Chloroplastida Chromosome Eukaryota Viridiplantae Streptophyta Liliopsida Poales Poaceae Sorghum Sorghum bicolor Musa acuminata subsp. malaccensis GCF_000313855.2 + 4641 AMA file_147 47707 47083 98,69 46081 96,59 Archaeplastida Chloroplastida Chromosome Eukaryota Viridiplantae Streptophyta Liliopsida Zingiberales Musaceae Musa Musa acuminata Aspergillus fumigatus Af293 GCF_000002655.1 + 746128 OAF file_148 9630 8617 89,48 4816 50,01 Opisthokonta Fungi Chromosome Eukaryota Fungi Ascomycota Eurotiomycetes Eurotiales Aspergillaceae Aspergillus Aspergillus fumigatus Entamoeba histolytica HM-1:IMSS GCF_000208925.1 + 5759 MEH file_149 8163 5168 63,31 5874 71,96 Mycetozoa Archamoeba Scaffold http://www.ncbi.nlm.nih.gov/bioproject/19739 - - Leishmania panamensis GCF_000755165.1 + 5679 ELP file_15 7748 7698 99,35 2571 33,18 Excavata Discoba Chromosome Eukaryota - - - Kinetoplastida Trypanosomatidae Leishmania Leishmania panamensis Magnaporthe oryzae 70-15 GCF_000002495.2 + 318829 OMO file_150 12989 9631 74,15 5843 44,98 Opisthokonta Fungi Chromosome Eukaryota Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Magnaporthe Magnaporthe oryzae Coccomyxa subellipsoidea C-169 GCF_000258705.1 + 248742 ACS file_151 9839 7950 80,80 5141 52,25 Archaeplastida Chloroplastida Contig ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Csubellipsoidea_C-169/ ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Csubellipsoidea_C-169/ ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Csubellipsoidea_C-169/ Callithrix jacchus GCF_000004665.1 + 9483 OCJ file_16 45251 44887 99,20 42697 94,36 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia Primates Cebidae Callithrix Callithrix jacchus Cryptococcus neoformans var. neoformans JEC21 GCF_000091045.1 + 5207 OCNNJ file_17 6475 6417 99,10 2869 44,31 Opisthokonta Fungi Chromosome Eukaryota Fungi Basidiomycota Tremellomycetes Tremellales Cryptococcaceae Cryptococcus Cryptococcus neoformans Encephalitozoon hellem ATCC 50504 GCF_000277815.2 + 27973 OEH file_18 1847 1842 99,73 429 23,23 Opisthokonta Fungi Chromosome Eukaryota Fungi Microsporidia - - Unikaryonidae Encephalitozoon Encephalitozoon hellem Ictalurus punctatus GCF_001660625.1 + 7998 OIP file_19 47974 47632 99,29 45961 95,80 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Actinopteri Siluriformes Ictaluridae Ictalurus Ictalurus punctatus Ananas comosus GCF_001540865.1 + 4615 AAC file_2 35775 34961 97,72 33646 94,05 Archaeplastida Chloroplastida Chromosome Eukaryota Viridiplantae Streptophyta Liliopsida Poales Bromeliaceae Ananas Ananas comosus Encephalitozoon intestinalis ATCC 50506 GCF_000146465.1 + 58839 OEI file_20 1938 1841 94,99 405 20,90 Opisthokonta Fungi Chromosome Eukaryota Fungi Microsporidia - - Unikaryonidae Encephalitozoon Encephalitozoon intestinalis Amphimedon queenslandica GCF_000090795.1 + 400682 OAQ file_21 24115 19061 79,04 20761 86,09 Opisthokonta Animalia Scaffold ftp://ftp.ncbi.nih.gov/genomes/Amphimedon_queenslandica/ ftp://ftp.ncbi.nih.gov/genomes/Amphimedon_queenslandica/ - Babesia bovis GCF_000165395.1 + 5865 SBBO file_22 3706 3444 92,93 1251 33,76 SAR Alveolata Chromosome Eukaryota - Apicomplexa Aconoidasida - Babesiidae Babesia Babesia bovis Equus caballus GCF_000002305.2 + 9796 OECA file_23 36064 35932 99,63 33252 92,20 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia Perissodactyla Equidae Equus Equus caballus Drosophila yakuba GCF_000005975.2 + 7245 ODY file_24 23317 23017 98,71 19168 82,21 Opisthokonta Animalia Chromosome Eukaryota Metazoa Arthropoda Insecta Diptera Drosophilidae Drosophila Drosophila yakuba Plasmodium vivax GCF_000002415.2 + 5855 SPV file_25 5392 4823 89,45 1963 36,41 SAR Alveolata Chromosome Eukaryota - Apicomplexa Aconoidasida Haemosporida Plasmodiidae Plasmodium Plasmodium vivax Trypanosoma brucei gambiense DAL972 GCF_000210295.1 + 5691 ETBG file_26 9822 8018 81,63 3101 31,57 Excavata Discoba Chromosome Eukaryota - - - Kinetoplastida Trypanosomatidae Trypanosoma Trypanosoma brucei Ostreococcus lucimarinus CCE9901 GCF_000092065.1 + 242159 AOL file_28 7603 7363 96,84 3419 44,97 Archaeplastida Chloroplastida Complete Genome Eukaryota Viridiplantae Chlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Ostreococcus Ostreococcus 'lucimarinus' Emiliania huxleyi CCMP1516 GCF_000372725.1 + 2903 HEH file_29 38554 24765 64,23 33655 87,29 Hacrobia Haptophyta Scaffold http://genome.jgi.doe.gov/Emihu1/download/ NC_005332 NC_007288 Chlorella variabilis GCF_000147415.1 + 554065 ACV file_3 9780 8700 88,96 5451 55,74 Archaeplastida Chloroplastida Scaffold ftp://ftp.jgi-psf.org/pub/JGI_data/Chlorella_NC64A/ - NC_015359 Drosophila simulans GCF_000754195.2 + 7240 ODS file_30 24132 23793 98,60 19741 81,80 Opisthokonta Animalia Chromosome Eukaryota Metazoa Arthropoda Insecta Diptera Drosophilidae Drosophila Drosophila simulans Piptocephalis cylindrospora RSA 2659 Pipcy3_1_GeneCatalog_proteins_20160615.aa.fasta.gz + 1907219 OPCY file_31 4301 3390 78,82 1476 34,32 Opisthokonta Fungi http://genome.jgi.doe.gov/Pipcy2/Pipcy2.home.html Eukaryota Fungi Zoopagomycota Zoopagales Piptocephalidaceae Piptocephalis Piromyces sp. E2 PirE2_1_GeneCatalog_proteins_20110421.aa.fasta.gz + 73868 OPE2 file_32 14648 12380 84,52 9054 61,81 Opisthokonta Fungi http://genome.jgi.doe.gov/PirE2_1 Eukaryota Fungi Chytridiomycota Neocallimastigomycetes Neocallimastigales Neocallimastigaceae Pecoramyces Tetrahymena thermophila SB210 GCF_000189635.1 + 5911 STT file_33 26996 15015 55,62 17854 66,14 SAR Alveolata Scaffold http://www.ciliate.org/system/downloads/ NC_003029 - Giardia lamblia ATCC 50803 GCF_000002435.1 + 5741 EGL file_34 6502 2656 40,85 2385 36,68 Excavata Metamonoada Scaffold http://giardiadb.org/common/downloads/release-3.1/GintestinalisAssemblageA/ - - Cryptococcus neoformans var. neoformans B-3501A GCF_000149385.1 + 5207 OCNNB file_35 6578 6570 99,88 2820 42,87 Opisthokonta Fungi Chromosome Eukaryota Fungi Basidiomycota Tremellomycetes Tremellales Cryptococcaceae Cryptococcus Cryptococcus neoformans Pongo abelii GCF_000001545.4 + 9601 OPA file_36 37232 36915 99,15 33383 89,66 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia Primates Hominidae Pongo Pongo abelii Volvox carteri Volvox_carteri.fasta.gz + 3067 AVC file_37 15286 11192 73,22 7652 50,06 Archaeplastida Micromonas commoda GCF_000090985.2 + 296587 AMC file_38 10137 8697 85,79 4553 44,91 Archaeplastida Chloroplastida Complete Genome Eukaryota Viridiplantae Chlorophyta Mamiellophyceae Mamiellales Mamiellaceae Micromonas Micromonas commoda Theileria parva GCF_000165365.1 + 5875 STP file_39 4061 3513 86,51 1259 31,00 SAR Alveolata Chromosome Eukaryota - Apicomplexa Aconoidasida - Theileriidae Theileria Theileria parva Pan paniscus GCF_000258655.2 + 9597 OPP file_4 47448 47180 99,44 44586 93,97 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia Primates Hominidae Pan Pan paniscus Saccharomyces cerevisiae S288C GCF_000146045.2 + 4932 OSC file_40 6002 4633 77,19 2823 47,03 Opisthokonta Fungi Complete Genome Eukaryota Fungi Ascomycota Saccharomycetes Saccharomycetales Saccharomycetaceae Saccharomyces Saccharomyces cerevisiae Zymoseptoria tritici IPO323 GCF_000219625.1 + 1047171 OZT file_41 10963 8355 76,21 5241 47,81 Opisthokonta Fungi Chromosome Eukaryota Fungi Ascomycota Dothideomycetes Capnodiales Mycosphaerellaceae Zymoseptoria Zymoseptoria tritici Neospora caninum Liverpool GCF_000208865.1 + 29176 SNC file_42 6936 6839 98,60 2368 34,14 SAR Alveolata Chromosome Eukaryota - Apicomplexa Coccidia Eucoccidiorida Sarcocystidae Neospora Neospora caninum Saprolegnia parasitica GCF_000151545.1 + 695850 SSP file_43 20121 15118 75,14 15042 74,76 SAR Stramenopiles Scaffold http://www.broadinstitute.org/annotation/genome/Saprolegnia_parasitica/ http://www.broadinstitute.org/annotation/genome/Saprolegnia_parasitica/ - Oryzias latipes GCF_000313675.1 + 8090 OOL file_44 40114 39874 99,40 37652 93,86 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Actinopteri Beloniformes Adrianichthyidae Oryzias Oryzias latipes Monosiga brevicollis MX1 GCF_000002865.3 + 81824 OMB file_45 9203 7216 78,41 4626 50,27 Opisthokonta Choanoflagellida Scaffold ftp://ftp.jgi-psf.org/pub/JGI_data/Monosiga_brevicollis/ NC_004309 - Anolis carolinensis GCF_000090745.1 + 28377 OAC file_46 34826 33477 96,13 31252 89,74 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata - Squamata Dactyloidae Anolis Anolis carolinensis Spizellomyces punctatus DAOM BR117 v1 GCF_000182565.1 + 645134 OSPU file_47 9422 7974 84,63 5052 53,62 Opisthokonta Fungi Scaffold ACOE00000000.1 Eukaryota Fungi Chytridiomycota Chytridiomycetes Spizellomycetales Spizellomycetaceae Spizellomyces Spizellomyces punctatus Backusella circina FSU 941 Bacci1_GeneCatalog_proteins_20130730.aa.fasta.gz + 1314798 OBC file_48 17039 15147 88,90 13601 79,82 Opisthokonta Fungi http://genome.jgi.doe.gov/Bacci1 Eukaryota Fungi Mucoromycota Mucorales Backusellaceae Backusella Backusella circina Aureococcus anophagefferens GCF_000186865.1 + 44056 SAA file_49 11520 9592 83,26 8143 70,69 SAR Stramenopiles Scaffold ftp://ftp.jgi-psf.org/pub/JGI_data/Aureococcus_anophagefferens/ ftp://ftp.jgi-psf.org/pub/JGI_data/Aureococcus_anophagefferens/ ftp://ftp.jgi-psf.org/pub/JGI_data/Aureococcus_anophagefferens/ Cyprinus carpio GCF_000951615.1 + 7962 OCC file_5 63928 63487 99,31 62297 97,45 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Actinopteri Cypriniformes Cyprinidae Cyprinus Cyprinus carpio Basidiobolus meristosporus CBS 931.73 Basme2finSC_GeneCatalog_proteins_20150701.aa.fasta.gz + 1314790 OBM file_50 16111 13422 83,31 13258 82,29 Opisthokonta Fungi http://genome.jgi.doe.gov/Basme2finSC Eukaryota Fungi Zoopagomycota Basidiobolomycetes Basidiobolales Basidiobolaceae Basidiobolus Basidiobolus meristosporus Cryptococcus neoformans var. grubii H99 GCF_000149245.1 + 5207 OCNG file_51 7826 7518 96,06 4140 52,90 Opisthokonta Fungi Chromosome Eukaryota Fungi Basidiomycota Tremellomycetes Tremellales Cryptococcaceae Cryptococcus Cryptococcus neoformans Chondrus crispus GCF_000350225.1 + 2769 ACC file_52 9807 5495 56,03 4374 44,60 Archaeplastida Rhodophyceae Genebank Scaffold ( GCA_000350225.2 ASM35022v2 ) http://www.ncbi.nlm.nih.gov/bioproject/193762 NC_001677 NC_020795 Drosophila miranda GCF_000269505.1 + 7229 ODMI file_53 22644 22481 99,28 18864 83,31 Opisthokonta Animalia Chromosome Eukaryota Metazoa Arthropoda Insecta Diptera Drosophilidae Drosophila Drosophila miranda Plasmodium falciparum 3D7 GCF_000002765.3 + 5833 SPF file_54 5337 4890 91,62 2163 40,53 SAR Alveolata Chromosome Eukaryota - Apicomplexa Aconoidasida Haemosporida Plasmodiidae Plasmodium Plasmodium falciparum Toxoplasma gondii ME49 GCF_000006565.2 + 5811 STG file_55 8318 7190 86,44 2714 32,63 SAR Alveolata Chromosome Eukaryota - Apicomplexa Coccidia Eucoccidiorida Sarcocystidae Toxoplasma Toxoplasma gondii Bathycoccus prasinos GCF_002220235.1 + 41875 ABP file_56 7900 7013 88,77 3236 40,96 Archaeplastida Chloroplastida Chromosome Eukaryota Viridiplantae Chlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Bathycoccus Bathycoccus prasinos Zea mays GCF_000005005.2 + 4577 AZM file_57 58286 54143 92,89 54838 94,08 Archaeplastida Chloroplastida Chromosome Eukaryota Viridiplantae Streptophyta Liliopsida Poales Poaceae Zea Zea mays Leishmania infantum JPCM5 GCF_000002875.2 + 5671 ELI file_58 8150 8137 99,84 2995 36,75 Excavata Discoba Chromosome Eukaryota - - - Kinetoplastida Trypanosomatidae Leishmania Leishmania infantum Cryptosporidium parvum Iowa II GCF_000165345.1 + 5807 SCP file_59 3805 2669 70,14 1031 27,10 SAR Alveolata Chromosome Eukaryota - Apicomplexa Coccidia Eucoccidiorida Cryptosporidiidae Cryptosporidium Cryptosporidium parvum Gonapodya prolifera JEL478 GCA_001574975.1 + 1344416 OGP file_6 13831 9307 67,29 7683 55,55 Opisthokonta Fungi Scaffold LSZK00000000 (Chang et al. 2015) Eukaryota Fungi Chytridiomycota Monoblepharidomycetes Monoblepharidales Gonapodyaceae Gonapodya Gonapodya prolifera Arabidopsis thaliana GCF_000001735.3 + 3702 AAT file_60 48350 44184 91,38 45485 94,07 Archaeplastida Chloroplastida Chromosome Oryza sativa Japonica Group GCF_001433935.1 + 4530 AOS file_61 41070 39245 95,56 38137 92,86 Archaeplastida Chloroplastida Chromosome Eukaryota Viridiplantae Streptophyta Liliopsida Poales Poaceae Oryza Oryza sativa Trypanosoma brucei brucei TREU927 GCF_000002445.1 + 5691 ETBB file_62 8712 8210 94,24 3312 38,02 Excavata Discoba Chromosome Eukaryota - - - Kinetoplastida Trypanosomatidae Trypanosoma Trypanosoma brucei Conidiobolus coronatus NRRL 28638 GCA_001566745.1 + 796925 OCCN file_63 10572 7013 66,34 6907 65,33 Opisthokonta Fungi Scaffold JXYT00000000 (Chang et al. 2015) Eukaryota Fungi Zoopagomycota Entomophthoromycetes Entomophthorales Ancylistaceae Conidiobolus Conidiobolus coronatus Coemansia reversa NRRL 1564 GCA_002705745.1 + 763665 OCR file_64 7341 6448 87,84 3472 47,30 Opisthokonta Fungi Scaffold JZJC00000000 (Chang et al. 2015) Eukaryota Fungi Zoopagomycota Kickxellales Kickxellaceae Coemansia Coemansia reversa Caenorhabditis elegans GCF_000002985.6 + 6239 OCE file_65 28167 25271 89,72 22739 80,73 Opisthokonta Animalia Complete Genome Eukaryota Metazoa Nematoda Chromadorea Rhabditida Rhabditidae Caenorhabditis Caenorhabditis elegans Gallus gallus GCF_000002315.4 + 9031 OGG file_66 46346 45712 98,63 44237 95,45 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Aves Galliformes Phasianidae Gallus Gallus gallus Mortierella verticillata NRRL 6337 GCA_000739165.1 + 1069443 OMV file_67 12595 9768 77,55 8521 67,65 Opisthokonta Fungi Scaffold AEVJ00000000.1 Eukaryota Fungi Mucoromycota Mortierellales Mortierellaceae Mortierella Mortierella verticillata Lepisosteus oculatus GCF_000242695.1 + 7918 OLO file_68 41647 41283 99,13 39314 94,40 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Actinopteri Semionotiformes Lepisosteidae Lepisosteus Lepisosteus oculatus Dictyostelium discoideum GCF_000004695.1 + 44689 MDD file_69 13315 9735 73,11 8391 63,02 Mycetozoa Dictyosteliida Chromosome Eukaryota - - - Dictyosteliida - Dictyostelium Dictyostelium discoideum Caenorhabditis briggsae GCF_000004555.1 + 6238 OCB file_7 19404 17754 91,50 13563 69,90 Opisthokonta Animalia Chromosome Eukaryota Metazoa Nematoda Chromadorea Rhabditida Rhabditidae Caenorhabditis Caenorhabditis briggsae Drosophila melanogaster GCF_000001215.4 + 7227 ODME file_70 30482 30347 99,56 27810 91,23 Opisthokonta Animalia Chromosome Eukaryota Metazoa Arthropoda Insecta Diptera Drosophilidae Drosophila Drosophila melanogaster Chromera velia CryptoDB-35_CveliaCCMP2878_AnnotatedProteins.fasta.gz + 1169474 SCV file_71 31799 16427 51,66 22096 69,49 SAR Alveolata Scaffold http://cryptodb.org/common/downloads/Current_Release/CveliaCCMP2878/ Chlamydomonas reinhardtii GCF_000002595.1 + 3055 ACR file_72 14488 11730 80,96 7910 54,60 Archaeplastida Chloroplastida Scaffold ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Creinhardtii/ NC_001638 NC_005353 Thermothelomyces thermophila ATCC 42464 GCF_000226095.1 + 78579 OTT file_73 9097 8098 89,02 3732 41,02 Opisthokonta Fungi Complete Genome Eukaryota Fungi Ascomycota Sordariomycetes Sordariales Chaetomiaceae Thermothelomyces Thermothelomyces thermophila Polysphondylium pallidum PN500 GCF_000004825.1 + 13642 MPP file_74 12336 9332 75,65 7674 62,21 Mycetozoa Dictyosteliida Scaffold http://genomes.dictybase.org/pallidum/ http://genomes.dictybase.org/pallidum/ - Gorilla gorilla gorilla GCF_000151905.2 + 9593 OGGG file_75 46533 46324 99,55 43743 94,00 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia Primates Hominidae Gorilla Gorilla gorilla Oryctolagus cuniculus GCF_000003625.3 + 9986 OOC file_76 38458 37972 98,74 35712 92,86 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia Lagomorpha Leporidae Oryctolagus Oryctolagus cuniculus Ustilago maydis 521 GCF_000328475.2 + 5270 OUM file_77 6783 5511 81,25 2592 38,21 Opisthokonta Fungi Chromosome Eukaryota Fungi Basidiomycota Ustilaginomycetes Ustilaginales Ustilaginaceae Ustilago Ustilago maydis Galdieria sulphuraria GCF_000341285.1 + 130081 AGS file_78 7174 5594 77,98 4249 59,23 Archaeplastida Rhodophyceae Scaffold http://www.ncbi.nlm.nih.gov/bioproject/221242 NC_024666 NC_024665 Monodelphis domestica GCF_000002295.2 + 13616 OMD file_79 49112 48478 98,71 46845 95,38 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia Didelphimorphia Didelphidae Monodelphis Monodelphis domestica Crassostrea virginica GCF_002022765.2 + 6565 OCV file_8 60213 48810 81,06 57356 95,26 Opisthokonta Animalia Chromosome Eukaryota Metazoa Mollusca Bivalvia Ostreoida Ostreidae Crassostrea Crassostrea virginica Salmo salar GCF_000233375.1 + 8030 OSS file_80 97555 96892 99,32 96291 98,70 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Actinopteri Salmoniformes Salmonidae Salmo Salmo salar Physcomitrella patens subsp. patens GCF_000002425.3 + 3218 APP file_81 35934 20263 56,39 26858 74,74 Archaeplastida Rhodophyceae Genebank Scaffold ( GCA_000002425.1 V1.1 ) ftp://ftp.ncbi.nlm.nih.gov/genomes/Physcomitrella_patens/ NC_007945 NC_005087 Naegleria gruberi GCF_000004985.1 + 5762 ENG file_82 15711 9837 62,61 10390 66,13 Excavata Discoba Scaffold http://genome.jgi.doe.gov/Naegr1/download/ http://genome.jgi.doe.gov/Naegr1/download/ - Phaseolus vulgaris GCF_000499845.1 + 3885 APV file_83 32720 30408 92,93 29292 89,52 Archaeplastida Chloroplastida Chromosome Eukaryota Viridiplantae Streptophyta - Fabales Fabaceae Phaseolus Phaseolus vulgaris Bos indicus GCF_000247795.1 + 9915 OBI file_84 35992 35822 99,53 33263 92,42 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia - Bovidae Bos Bos indicus Taeniopygia guttata GCF_000151805.1 + 59729 OTG file_85 19443 19372 99,63 16695 85,87 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Aves Passeriformes Estrildidae Taeniopygia Taeniopygia guttata Ostreococcus tauri GCF_000214015.3 + 70448 AOT file_86 7766 7422 95,57 3388 43,63 Archaeplastida Chloroplastida Chromosome Eukaryota Viridiplantae Chlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Ostreococcus Ostreococcus tauri Oxytricha trifallax (no assembly file) Oxtri.aa.fasta.gz 1172189 SOT file_87 24885 14515 58,33 19321 77,64 SAR Alveolata not in refseq http://oxy.ciliate.org/system/downloads/ http://oxy.ciliate.org/system/downloads/ - Selaginella moellendorffii GCF_000143415.3 + 88036 ASM file_88 34746 29994 86,32 33754 97,14 Archaeplastida Chloroplastida Scaffold ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Smoellendorffii/ - NC_013086 Leishmania donovani GCF_000227135.1 + 5661 ELD file_89 8032 7953 99,02 2750 34,24 Excavata Discoba Chromosome Eukaryota - - - Kinetoplastida Trypanosomatidae Leishmania Leishmania donovani Bigelowiella natans CCMP2755 Bigna1_filtered_proteins.fasta.gz + 753081 SBN file_9 21708 13689 63,06 11189 51,54 SAR Rhizaria not in refseq/ Genbank Contig (GCA_000320545.1) http://genome.jgi.doe.gov/Bigna1/download/ - NC_008408 Blastocystis hominis GCF_000151665.1 + 12968 SBH file_90 6020 4713 78,29 3426 56,91 SAR Stramenopiles Scaffold https://www.genoscope.cns.fr/externe/Download/Projets/Blastocystis/ - - Fusarium graminearum PH-1 GCF_000240135.3 + 5518 OFG file_91 13313 10908 81,93 6647 49,93 Opisthokonta Fungi Chromosome Eukaryota Fungi Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusarium Fusarium graminearum Ramicandelaber brevisporus CBS 109374 Rambr1_GeneCatalog_proteins_20140929.aa.fasta.gz + 304332 ORB file_92 9281 6212 66,93 5539 59,68 Opisthokonta Fungi http://genome.jgi.doe.gov/Rambr1 Eukaryota Fungi Zoopagomycota Kickxellales Kickxellaceae Ramicandelaber Phytophthora sojae GCF_000149755.1 + 67593 SPS file_93 26489 16102 60,79 21088 79,61 SAR Stramenopiles Scaffold http://genome.jgi.doe.gov/Physo3/download/ NC_009385 - Umbelopsis ramanniana NRRL 5844 Umbra1_GeneCatalog_proteins_20121109.aa.fasta.gz + 979654 OUR file_94 9931 8649 87,09 5539 55,77 Opisthokonta Fungi http://genome.jgi.doe.gov/Umbra1 Eukaryota Fungi Mucoromycota Umbelopsidales Umbelopsidaceae Umbelopsis Drosophila busckii GCF_001277935.1 + 30019 ODB file_95 20692 20372 98,45 16961 81,97 Opisthokonta Animalia Chromosome Eukaryota Metazoa Arthropoda Insecta Diptera Drosophilidae Drosophila Drosophila busckii Martensiomyces pterosporus CBS 209.56 Marpt1_GeneCatalog_proteins_20140919.aa.fasta.gz + 61414 OMP file_96 8435 7147 84,73 4218 50,01 Opisthokonta Fungi http://genome.jgi.doe.gov/Marpt1 Eukaryota Fungi Zoopagomycota Kickxellales Kickxellaceae Martensiomyces Felis catus GCF_000181335.3 + 9685 OFC file_97 54726 41083 75,07 39736 72,61 Opisthokonta Animalia Chromosome Eukaryota Metazoa Chordata Mammalia Carnivora Felidae Felis Felis catus Cryptococcus gattii WM276 GCF_000185945.1 + 37769 OCG file_98 6561 6325 96,40 2524 38,47 Opisthokonta Fungi Chromosome Eukaryota Fungi Basidiomycota Tremellomycetes Tremellales Cryptococcaceae Cryptococcus Cryptococcus gattii VGI Reticulomyxa filosa GCA_000512085.1 + 46433 SRF file_99 39963 16185 40,50 29419 73,62 SAR Rhizaria Scaffold