OrthoDB Species

Tue, 10/04/2011 - 09:58

166 Species: 48 Vertebrates, 33 Arthropods,
73 Fungi, and 12 basal Metazoans


Email: support[at]orthodb.org

48 Vertebrates

Input Genes
Lineage Species Count Total Average Std. Dev.
Vertebrates 48 862,025 17,959 3,008
    Species Common Name Genome Assembly Genebuild Gene Count
  • Actinopterygii (Ray-Finned Fishes):
    Danio rerio Zebrafish Zv9, Apr 2010 Nov 2010 26095
    Oryzias latipes Medaka (ricefish) HdrR, Oct 2005 Oct 2006 19686
    Gasterosteus aculeatus Stickleback BROAD S1, Feb 2006 Aug 2006 20787
    Tetraodon nigroviridis Pufferfish (green spotted) TETRAODON 8.0, Mar 2007 Jul 2008 19602
    Takifugu rubripes Pufferfish (fugu) FUGU 4.0, Jun 2005 Mar 2008 18523
  • Amphibia (Amphibians):
    Xenopus tropicalis Western Clawed Frog JGI 4.2, Nov 2009 Feb 2011 18429
  • Sauropsida (Reptiles & Birds):
    Anolis carolinensis Anole Lizard AnoCar2.0, May 2010 Dec 2010 17792
    Taeniopygia guttata Zebra Finch Taeniopygia_guttata-3.2.4, Aug 2008 Feb 2009 17475
    Meleagris gallopavo Common Turkey Turkey_2.01, Sep 2010 Dec 2010 14112
    Gallus gallus Chicken WASHUC2, May 2006 Dec 2006 16736
  • Monotremata (Monotremes):
    Ornithorhynchus anatinus Platypus Ornithorhynchus_anatinus-5.0, Dec 2005 Aug 2007 17951
  • Marsupialia (Marsupials):
    Macropus eugenii Wallaby Meug_1.0, Dec 2008 Jun 2009 15290
    Monodelphis domestica Opossum monDom5, Oct 2006 Apr 2007 19466
  • Afrotheria (Tenrecs, Aardvarks, Hyraxes, Elephants & Sea Cows):
    Echinops telfairi Tenrec Hedgehog TENREC, Jul 2005 Aug 2006 16562
    Procavia capensis Rock Hyrax proCap1, Jul 2008 Feb 2009 16044
    Loxodonta africana African Elephant Loxafr3.0, Jul 2009 Mar 2010 20020
  • Xenarthra (Anteaters, Sloths, & Armadillos):
    Dasypus novemcinctus Nine-banded Armadillo dasNov2, Jul 2008 Feb 2009 14803
    Choloepus hoffmanni Hoffmann's two-fingered sloth choHof1, Sep 2008 Feb 2009 12393
  • Laurasiatheria (Shrews, Hedgehogs, Bats, Whales, Hoofed Mammals, & Carnivorans):
    Sorex araneus Common Shrew sorAra1, Oct 2005 Jun 2007 13187
    Erinaceus europaeus European Hedgehog eriEur1, Jun 2006 Feb 2007 14588
    Pteropus vampyrus Flying Fox (bat) pteVam1, Jul 2008 Feb 2009 16990
    Myotis lucifugus Little Brown Bat Myoluc2.0, Sep 2010 Jun 2011 19728
    Felis catus Cat CAT, Mar 2006 Jul 2008 15048
    Canis familiaris Dog CanFam 2.0, May 2006 Dec 2006 19305
    Ailuropoda melanoleuca Giant Panda ailMel1, Jul 2009 Oct 2010 19330
    Equus caballus Horse Equ Cab 2, Sep 2007 Mar 2008 20436
    Vicugna pacos Alpaca vicPac1, Jul 2008 Feb 2009 11752
    Sus scrofa Pig Sscrofa9, Apr 2009 Sep 2009 17493
    Bos taurus Cow Btau_4.0, Oct 2007 Jul 2008 21048
    Tursiops truncatus Bottlenose Dolphin turTru1, Jul 2008 Feb 2009 16537
  • Glires (Lagomorphs & Rodents):
    Ochotona princeps American Pika OchPri2.0, Jun 2007 Jul 2008 15993
    Oryctolagus cuniculus European Rabbit oryCun2, Nov 2009 Mar 2010 19005
    Spermophilus tridecemlineatus Squirrel speTri1, Jun 2006 Apr 2007 14827
    Cavia porcellus Guinea Pig cavPor3, Mar 2008 Sep 2008 18673
    Dipodomys ordii Kangaroo Rat dipOrd1, Jul 2008 Feb 2009 15798
    Rattus norvegicus Rat RGSC 3.4, Dec 2004 Sep 2009 22938
    Mus musculus Mouse NCBIM37, Apr 2007 Jan 2011 23041
  • Euarchonta (Scandentia, Dermoptera, & Primates):
    Tupaia belangeri Treeshrew tupBel1, Jun 2006 Feb 2007 15458
    Otolemur garnettii Greater Galago otoGar1, May 2006 Apr 2007 15443
    Microcebus murinus Gray Mouse Lemur micMur1, Jun 2007 Mar 2008 16319
    Tarsius syrichta Philippine Tarsier tarSyr1, Jul 2008 Feb 2009 13615
    Callithrix jacchus Marmoset C_jacchus3.2.1, Jan 2010 May 2010 20993
    Macaca mulatta Rhesus Macaque MMUL 1.0, Feb 2006 Aug 2006 21905
    Nomascus leucogenys Northern white-cheeked gibbon Nleu1.0, Jan 2010 Apr 2011 18161
    Pongo pygmaeus Orangutan PPYG2, Sep 2007 Mar 2008 20068
    Gorilla gorilla Gorilla gorGor3, Dec 2009 Mar 2010 20962
    Pan troglodytes Chimpanzee CHIMP2.1, Mar 2006 Jul 2008 19829
    Homo sapiens Human GRCh37.p3, Feb 2009 Apr 2011 21789



33 Arthropods

Input Genes
Lineage Species Count Total Average Std. Dev.
Arthropods 33 572,882 17,360 6,468
    Species Common Name Genome Assembly Genebuild Gene Count
  • Arachnida:
    Ixodes scapularis Tick IscaW1 IscaW1.1, Dec 2008 20486
  • Crustacea:
    Daphnia pulex Water Flea JGI060905 Gene Set 2.0 beta3, Apr 2010 47712
  • Hemipterodea:
    Zootermopsis nevadensis
    (Gene set not yet available for download)    		 Rottenwood Termite 2.1 17737
    Pediculus humanus Body Louse PhumU1 PhumU1.2, Jul 2009 10772
    Acyrthosiphon pisum Aphid Assembly version 2 ACYPI v2.0 31482
  • Hymenoptera:
    Nasonia vitripennis Parasitoid Wasp Nvit_1.0 OGS_v1.2 18731
    Bombus terrestris Bumble Bee 1.0 GNOMON 12694
    Apis mellifera Honey Bee Assembly 2 Amel_pre_release2 10699
    Harpegnathos saltator Jumping Ant Assembly1 3.5 18564
    Linepithema humile Argentine Ant Assembly1 1.2 16048
    Camponotus floridanus Carpenter Ant Assembly1 3.5 17062
    Pogonomyrmex barbatus Harvester Ant Assembly1 1.2 17108
    Solenopsis invicta Fire Ant 2.2.3 16522
    Acromyrmex echinatior Panamanian Leaf-cutter Ant 3.8 17278
    Atta cephalotes Leaf-cutter Ant 1.2 18062
  • Coleoptera:
    Tribolium castaneum Flour Beetle Tcas 3.0 Tcas 3.0 16565
  • Lepidoptera:
    Bombyx mori Silkmoth Silkworm_genome_v2.0 GLEAN set 14623
  • Diptera:
    Anopheles gambiae Mosquitoes AgamP3 AgamP3.6, Dec 2010 12670
    Aedes aegypti Mosquitoes AaegL1 AaegL1.2, Sep 2009 15986
    Culex quinquefasciatus Mosquitoes CpipJ1 CpipJ1.2, Jun 2008 18882
    Mayetiola destructor Hessian Fly 18768
    Drosophila grimshawi Fruitflies 1 1.3 14982
    Drosophila mojavensis Fruitflies 1 1.3 14594
    Drosophila virilis Fruitflies 1 1.2 14491
    Drosophila willistoni Fruitflies 1 1.3 15512
    Drosophila persimilis Fruitflies 1 1.3 16874
    Drosophila pseudoobscura Fruitflies 2 2.23 16001
    Drosophila ananassae Fruitflies 1 1.3 15069
    Drosophila erecta Fruitflies 1 1.3 15044
    Drosophila yakuba Fruitflies 1 1.3 16077
    Drosophila melanogaster Fruitflies 5 5.40 13907
    Drosophila sechellia Fruitflies 1 1.3 16467
    Drosophila simulans Fruitflies 1 1.3 15413



12 Basal Metazoans



73 Fungi

Input Genes
Lineage Species Count Total Average Std. Dev.
Fungi 73 650,230 8,907 3,893



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