OrthoDB Species

252 Eukaryotic Species:
52 Vertebrates, 45 Arthropods,
142 Fungi, and 13 basal Metazoans.
1115 Bacteria


Email: support[at]orthodb.org

52 Vertebrates

((DRERI,(GMORH,((OLATI,ONILO),(GACUL,(TNIGR,TRUBR))))),(LCHAL,(XTROP,((ACARO,(TGUTT,(MGALL,GGALL))),(OANAT,((MDOME,(MEUGE,SHARR)),(((DNOVE,CHOFF),(ETELF,(PCAPE,LAFRI))),(((SARAN,EEURO),(((PVAMP,MLUCI),(ECABA,(FCATU,(CFAMI,AMELA)))),(VPACO,(SSCRO,(BTAUR,TTRUN))))),(((OPRIN,OCUNI),(STRID,(CPORC,(DORDI,(RNORV,MMUSC))))),(TBELA,((OGARN,MMURI),(TSYRI,(CJACC,(MMULA,(NLEUC,(PABEL,(GGORI,(PTROG,HSAPI))))))))))))))))));

Input Genes
Lineage Species Count Total Average Std. Dev.
Vertebrates 52 951,242 18,293 2,894
    Species Common Name Genome Assembly Genebuild Gene Count
  • Actinopterygii (Ray-Finned Fishes):
    Danio rerio Zebrafish Zv9, Apr 2010 Mar 2012 26206
    Gadus morhua Atlantic cod gadMor1, Jan 2010 Aug 2011 20095
    Oryzias latipes Medaka fish HdrR, Oct 2005 May 2010 19686
    Oreochromis niloticus Nile tilapia Orenil1.0, Jan 2011 Mar 2012 21437
    Gasterosteus aculeatus Three-spined stickleback BROAD S1, Feb 2006 May 2010 20787
    Tetraodon nigroviridis Spotted green pufferfish TETRAODON 8.0, Mar 2007 May 2010 19602
    Takifugu rubripes Japanese pufferfish FUGU 4.0, Jun 2005 May 2010 18523
  • Coelacanthiformes:
    Latimeria chalumnae West Indian ocean coelacanth LatCha1, Sep 2011 Mar 2012 19567
  • Amphibia (Amphibians):
    Xenopus tropicalis Western clawed frog JGI 4.2, Nov 2009 Feb 2011 18429
  • Sauropsida (Reptiles & Birds):
    Anolis carolinensis Green anole lizard AnoCar2.0, May 2010 Dec 2011 17805
    Taeniopygia guttata Zebra finch Taeniopygia_guttata-3.2.4, Aug 2008 May 2012 17488
    Meleagris gallopavo Common turkey Turkey_2.01, Sep 2010 Dec 2011 14125
    Gallus gallus Chicken WASHUC2, May 2006 May 2010 16736
  • Monotremata (Monotremes):
    Ornithorhynchus anatinus Duckbill platypus Ornithorhynchus_anatinus-5.0, Dec 2005 May 2010 17951
  • Marsupialia (Marsupials):
    Monodelphis domestica Gray short-tailed opossum monDom5, Oct 2006 May 2010 19466
    Macropus eugenii Trammar wallaby Meug_1.0, Dec 2008 May 2010 15290
    Sarcophilus harrisii Tasmanian devil Devil_ref v7.0, Mar 2011 Dec 2011 18788
  • Xenarthra (Anteaters, Sloths, & Armadillos):
    Dasypus novemcinctus Nine-banded armadillo dasNov2, Jul 2008 May 2010 14803
    Choloepus hoffmanni Hoffmann's two-fingered sloth choHof1, Sep 2008 May 2010 12393
  • Afrotheria (Tenrecs, Aardvarks, Hyraxes, Elephants & Sea Cows):
    Echinops telfairi Lesser hedgehog tenrec TENREC, Jul 2005 May 2010 16562
    Procavia capensis Cape hyrax proCap1, Jul 2008 May 2010 16044
    Loxodonta africana African elephant Loxafr3.0, Jul 2009 Dec 2011 20033
  • Laurasiatheria (Shrews, Hedgehogs, Bats, Whales, Hoofed Mammals, & Carnivorans):
    Sorex araneus Eurasian common shrew sorAra1, Oct 2005 May 2010 13187
    Erinaceus europaeus Western European hedgehog eriEur1, Jun 2006 May 2010 14588
    Pteropus vampyrus Large flying fox pteVam1, Jul 2008 May 2010 16990
    Myotis lucifugus Little brown bat Myoluc2.0, Sep 2010 Jun 2011 19728
    Equus caballus Horse Equ Cab 2, Sep 2007 May 2010 20436
    Felis catus Cat CAT, Mar 2006 May 2010 15048
    Canis familiaris Dog CanFam 2.0, May 2006 May 2010 19305
    Ailuropoda melanoleuca Giant panda ailMel1, Jul 2009 Dec 2011 19343
    Vicugna pacos Alpaca vicPac1, Jul 2008 May 2010 11752
    Sus scrofa Pig Sscrofa10.2, Aug 2011 May 2012 21640
    Bos taurus Bovine UMD3.1, Nov 2009 Sep 2011 19994
    Tursiops truncatus Atlantic bottle-nosed dolphin turTru1, Jul 2008 May 2010 16537
  • Glires (Lagomorphs & Rodents):
    Ochotona princeps Southern American pika OchPri2.0, Jun 2007 May 2010 15993
    Oryctolagus cuniculus Rabbit oryCun2, Nov 2009 Dec 2011 19018
    Spermophilus tridecemlineatus Thirteen-lined ground squirrel spetri2, Nov 2011 May 2012 18826
    Cavia porcellus Guinea pig cavPor3, Mar 2008 May 2010 18673
    Dipodomys ordii Ords kangaroo rat dipOrd1, Jul 2008 May 2010 15798
    Rattus norvegicus Rat RGSC 3.4, Dec 2004 May 2010 22938
    Mus musculus Mouse NCBIM37, Apr 2007 Mar 2012 23075
  • Euarchonta (Scandentia, Dermoptera, & Primates):
    Tupaia belangeri Common tree shrew tupBel1, Jun 2006 May 2010 15458
    Otolemur garnettii Small-eared galago OtoGar3, Mar 2011 Dec 2011 19506
    Microcebus murinus Lesser mouse lemur micMur1, Jun 2007 May 2010 16319
    Tarsius syrichta Philippine tarsier tarSyr1, Jul 2008 May 2010 13615
    Callithrix jacchus White-tufted-ear marmoset C_jacchus3.2.1, Jan 2010 Mar 2011 20993
    Macaca mulatta Rhesus macaque MMUL 1.0, Feb 2006 May 2010 21905
    Nomascus leucogenys Northern white-cheeked gibbon Nleu1.0, Jan 2010 Apr 2011 18161
    Pongo abelii Sumatran orangutan PPYG2, Sep 2007 May 2010 20068
    Gorilla gorilla Lowland gorilla gorGor3, Dec 2009 Mar 2010 20962
    Pan troglodytes Chimpanzee CHIMP2.1.4, Feb 2011 Dec 2011 18746
    Homo sapiens Human GRCh37.p3, Feb 2009 May 2012 20824



45 Arthropods

((ISCAP,TURTI),(SMARI,(DPULE,(ZNEVA,((PHUMA,(RPROL,APISU)),((NVITR,((MROTU,((BIMPA,BTERR),(AFLOR,AMELL))),(HSALT,(LHUMI,(CFLOR,(PBARB,(SINVI,(AECHI,ACEPH)))))))),((TCAST,MMOLD),(((BMORI,MSEXT),(DPLEX,HMELP)),(((ADARL,(AGAMB,ASTEP)),(AAEGY,CQUIN)),(MDEST,((DGRIM,(DMOJA,DVIRI)),(DWILL,((DPERS,DPSEU),(DANAN,((DEREC,DYAKU),(DMELA,(DSECH,DSIMU)))))))))))))))));

Input Genes
Lineage Species Count Total Average Std. Dev.
Arthropods 45 746,324 16,585 4,816



13 Basal Metazoans

(TADHA,((NVECT,HMAGN),(((LGIGA,(CTELE,HROBU)),((CELEG,CBRIG),((ISCAP,TURTI),(SMARI,(DPULE,(ZNEVA,((PHUMA,(RPROL,APISU)),((NVITR,((MROTU,((BIMPA,BTERR),(AFLOR,AMELL))),(HSALT,(LHUMI,(CFLOR,(PBARB,(SINVI,(AECHI,ACEPH)))))))),((TCAST,MMOLD),(((BMORI,MSEXT),(DPLEX,HMELP)),(((ADARL,(AGAMB,ASTEP)),(AAEGY,CQUIN)),(MDEST,((DGRIM,(DMOJA,DVIRI)),(DWILL,((DPERS,DPSEU),(DANAN,((DEREC,DYAKU),(DMELA,(DSECH,DSIMU))))))))))))))))))),((CINTE,CSAVI),(SPURP,(BFLOR,(PMARI,((DRERI,(GMORH,((OLATI,ONILO),(GACUL,(TNIGR,TRUBR))))),(LCHAL,(XTROP,((ACARO,(TGUTT,(MGALL,GGALL))),(OANAT,((MDOME,(MEUGE,SHARR)),(((DNOVE,CHOFF),(ETELF,(PCAPE,LAFRI))),(((SARAN,EEURO),(((PVAMP,MLUCI),(ECABA,(FCATU,(CFAMI,AMELA)))),(VPACO,(SSCRO,(BTAUR,TTRUN))))),(((OPRIN,OCUNI),(STRID,(CPORC,(DORDI,(RNORV,MMUSC))))),(TBELA,((OGARN,MMURI),(TSYRI,(CJACC,(MMULA,(NLEUC,(PABEL,(GGORI,(PTROG,HSAPI)))))))))))))))))))))))));

Input Genes
Lineage Species Count Total Average Std. Dev.
Basal Metazoans 13 277,378 21,337 7,697



142 Fungi

(((NEMS1,(NEMP1,NEMP3)),(ENTBH,(NOSCE,(ENCCU,ENCIT)))),(((((MELLP,PUCGT),(MIXOS,RHOG2)),((MALGO,(SPORE,USTMA)),((CRYGW,(CRYNB,CRYNJ)),(PIRID,(SCHCM,(((SERL3,SERL9),POSPM),((COPC7,LACBS),MONPE))))))),(BATDJ,RHIO9)),((SCHJY,SCHPO),((YARLI,((((((TETPH,VANPO),TETBL),((KAZAF,(NAUCC,NAUDC)),(CANGA,((((YEAS8,(YEASV,YEASL)),((YEASO,YEASB),YEASZ)),(YEAS1,(YEAS2,(YEAST,(YEAS7,YEASK))))),(YEAS6,YEASA))))),(TORDC,ZYGRC)),(LACTC,(ASHGO,KLULA))),((CLAL4,(CANTC,((PICGU,(DEBHA,PICSO)),(PICST,(SPAPN,((LODEL,(CANO9,CANPC)),(CANTT,(CANDC,(CANAL,CANAW))))))))),(PICAD,(PICP7,PICPG))))),((ARTOA,TUBMM),(((((((NECH7,(FUSOF,GIBZE)),((HYPAI,(HYPJQ,HYPVG)),((METAQ,METAR),CORMM))),((VERA1,VERDV),(COLGM,COLHI))),(((SORMK,(NEUCR,(NEUT8,NEUT9))),(PODAN,(CHATD,(THITE,(CHAGB,THIHA))))),(GROCL,MAGO7))),(GLAL7,(SCLS1,(BOTF4,BOTFB)))),(MYCGM,(PHANO,(LEPMJ,(PYRTR,PYRTT))))),(EXODN,((((PARBA,(PARBD,PARBP)),((AJEDA,(AJEDS,AJEDR)),(AJECN,(AJECG,(AJEC8,AJECH))))),((ARTOC,(ARTGP,((TRIEC,TRIT1),(TRIRC,(ARTBC,TRIVH))))),(UNCRE,(COCP7,COCPS)))),((PENMQ,TALSN),(PENCW,((ASPCL,(NEOFI,(ASPFC,ASPFU))),(((ASPKW,(ASPNA,ASPNC)),(ASPTN,(ASPFN,ASPOR))),EMENI))))))))))));

Input Genes
Lineage Species Count Total Average Std. Dev.
Fungi 142 1,223,848 8,619 3,721



1115 Bacteria

Input Genes
Lineage Species Count Total Average Std. Dev.
Bacteria 1,115 3,532,434 3,168 1,652
Actinobacteria-Actinobacteria 119 411,905 3,461 1,933
Cyanobacteria-Chroococcales 20 75,315 3,766 1,663
Cyanobacteria-Prochlorales 12 24,597 2,050 341
Firmicutes-Bacilli 229 575,988 2,515 1,138
Firmicutes-Clostridia 54 167,344 3,099 865
Proteobacteria-Alphaproteobacteria 118 413,625 3,505 1,993
Proteobacteria-Betaproteobacteria 72 341,246 4,740 1,768
Proteobacteria-Gammaproteobacteria 237 885,079 3,735 1,370
Spirochaetes-Spirochaetia 18 38,276 2,126 1,240
Tenericutes-Mollicutes 25 17,955 718 189
Thermotogae-Thermotogae 11 20,806 1,891 115



Creative Commons Licence   This work by E Zdobnov lab is licensed under a Creative Commons Attribution 3.0 Unported License.