Genomicus v94.01 Title
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DYOGEN group

web-code version: 2017-06-13
database version: 94.01
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Statistics on modern & ancestral genomes


Genomicus 94.01 contains 2854494 genes from 141 extant species. This data was analysed with a new method called AGORA (Algorithm for Gene Order Reconstruction in Ancestors; Muffato et al. in preparation) to identify 2694537 ancestral genes from 120 ancestral species, grouped into 55523 blocks of collinear genes.

The following tables present statistics on the data used in Genomicus, and on the reconstructed blocks in the ancestral species.

  1. For extant species, a "contig" means a segment of the genome sequence assembly (chromosomes, scaffolds, contig) with at least two genes.
  2. The average block length, the N25, N50 and N75 values do not take into account the singletons (blocks of one gene).
 
Primates Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Angola colobus(extant sp.)2046761533.16611499.4%
Black snub-nosed monkey(extant sp.)20824149513.324100295.2%
Bolivian squirrel monkey(extant sp.)1929026772.11465099.7%
Bushbaby(extant sp.)1950637451.811515199.2%
Capuchin(extant sp.)2020083224.05120199.0%
Chimpanzee(extant sp.)2330225091.896335198.5%
Coquerels sifaka(extant sp.)1788462428.45318499.0%
Crab-eating macaque(extant sp.)2140473290.5115419899.1%
Drill(extant sp.)20660121416.83131498.5%
Gibbon(extant sp.)20648108189.182122498.9%
Golden snub-nosed monkey(extant sp.)21132176311.42098695.3%
Gorilla(extant sp.)2158754394.8100426698.8%
Human(extant sp.)2240726384.98777699.7%
Marmoset(extant sp.)1956356346.699715699.2%
Mas night monkey(extant sp.)2032063031.86526398.7%
Mouse lemur(extant sp.)1881644427.07372999.8%
Olive baboon(extant sp.)21464131161.8113826998.7%
Orangutan(extant sp.)2042453385.48430100.0%
Pig-tailed macaque(extant sp.)2087234160.911710099.5%
Rhesus(extant sp.)2109958356.9111840098.1%
Sooty mangabey(extant sp.)2074641549.710712799.4%
Tarsier(extant sp.)1830432584.86261685.7%
Vervet Monkey(extant sp.)1916554353.76966599.7%
pygmy chimpanzee(extant sp.)2104171294.294615399.3%
 
Rodents etc. Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Brazilian-Guinea pig(extant sp.)1421823560.41823599.8%
Chinese hamster CHOK1GS(extant sp.)20824130159.160614699.3%
Chinese hamster Crigri(extant sp.)1961719979.316113494.2%
Damara mole rat(extant sp.)1773072824.15020298.9%
Degu(extant sp.)1998239650.111313099.3%
Golden Hamster(extant sp.)1825731257.011046597.5%
Guinea pig(extant sp.)1809525869.92146199.7%
Kangaroo rat(extant sp.)1691128957.710823998.6%
Lesser Egyptian jerboa(extant sp.)1784523874.71287799.6%
Long-tailed chinchilla(extant sp.)1780921283.71546999.6%
Mouse(extant sp.)2231694237.3110810100.0%
Naked mole-rat female(extant sp.)2077427475.51589299.6%
Naked mole-rat male(extant sp.)20742196510.21871496.6%
Northern American deer mouse(extant sp.)19854102519.03939998.0%
Pika(extant sp.)1600630103.94439772.5%
Prairie vole(extant sp.)1913019299.14849799.5%
Rabbit(extant sp.)1929358132.467847297.6%
Rat(extant sp.)2224555403.013117899.6%
Ryukyu mouse(extant sp.)1920820960.49640100.0%
Shrew mouse(extant sp.)1906124794.29250100.0%
Squirrel(extant sp.)1847448637.69021298.9%
Tree shrew(extant sp.)1547131623.34508767.1%
Upper Galilee mountains blind mole rat(extant sp.)18647107917.03035498.1%
spretus(extant sp.)1947620973.810440100.0%
 
Laurasiatherias Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Alpaca(extant sp.)1176520064.45299974.5%
Cat(extant sp.)1940962311.910876999.6%
Common shrew(extant sp.)1318719652.73794639.7%
Cow(extant sp.)1999432624.57791199.9%
Dog(extant sp.)1985681243.360615299.2%
Dolphin(extant sp.)1655031794.45247285.1%
Ferret(extant sp.)1991050339.09627698.6%
Giant Panda(extant sp.)19343181910.21879995.9%
Goat(extant sp.)21343151137.373561197.1%
Hedgehog(extant sp.)1460121052.42960634.2%
Horse(extant sp.)2044960340.17504699.8%
Megabat(extant sp.)1699031874.35319881.2%
Microbat(extant sp.)19728124914.939116994.1%
Pig(extant sp.)22342194114.5128212799.4%
Sheep(extant sp.)20921117174.087056497.3%
Tiger(extant sp.)1754450634.5626299.6%
leopard(extant sp.)1964630164.617119699.0%
 
Xenarthras etc. Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Armadillo(extant sp.)2271125548.313144893.6%
Sloth(extant sp.)1239311812.22977821.1%
 
Afrotherias etc. Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Elephant(extant sp.)2003335555.823022898.9%
Hyrax(extant sp.)1605728342.93778351.5%
Tenrec(extant sp.)1657525592.621004739.4%
 
Marsupials & Monotremes Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Opossum(extant sp.)21327111938.828700100.0%
Platypus(extant sp.)2169818556.822913857.9%
Tasmanian devil(extant sp.)1878819668.715165491.2%
Wallaby(extant sp.)1529017202.421111927.3%
 
Birds & Reptiles Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Chicken(extant sp.)1834651033.3517138792.4%
Chinese turtle(extant sp.)18189146711.92372696.0%
Duck(extant sp.)15634138110.517113592.7%
Flycatcher(extant sp.)1530349130.59233497.8%
Lizard(extant sp.)18595105516.3868137092.6%
Turkey(extant sp.)1412314097.250551096.4%
Zebra finch(extant sp.)1748868257.27121100.0%
 
Amphibians Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Frog(extant sp.)18442133913.12390295.1%
 
Fish Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Amazon molly(extant sp.)2361599723.25250997.8%
Asian bonytongue(extant sp.)2379729181.417210999.5%
Ballan wrasse(extant sp.)27270225411.036250590.8%
Bicolor damselfish(extant sp.)2308023139.81552597.7%
Big-finned mudskipper(extant sp.)2225223738.716166892.5%
Burton's mouthbrooder(extant sp.)23044112219.84686696.2%
Cave fish(extant sp.)2666288729.567148298.2%
Channel catfish(extant sp.)23598104223.484136998.4%
Climbing perch(extant sp.)2460348512.411908100.0%
Clown anemonefish(extant sp.)2355526618.51391396.1%
Cod(extant sp.)2009527166.410266386.7%
Eastern happy(extant sp.)26983139193.811875099.8%
Fugu(extant sp.)2051658933.269895995.3%
Greater amberjack(extant sp.)2324132072.220815299.3%
Guppy(extant sp.)22857129174.693433298.5%
Indian medaka(extant sp.)2351029578.075949497.9%
Japanese Medaka HNI(extant sp.)2212124921.79500100.0%
Japanese Medaka HSOK(extant sp.)2276924948.79780100.0%
Japanese Medaka HdrR(extant sp.)2360025944.09930100.0%
Lyretail cichlid(extant sp.)2356846849.115759097.5%
Mangrove rivulus(extant sp.)21911100621.18965297.0%
Midas cichlid(extant sp.)23675122618.84361697.4%
Monterrey platyfish(extant sp.)2054925822.08440100.0%
Mummichog(extant sp.)23054137715.935111695.2%
Northern pike(extant sp.)23925231103.193811999.5%
Ocean sunfish(extant sp.)21397147144.631914699.3%
Orange clownfish(extant sp.)2387231768.710344199.8%
P. kingsleyae(extant sp.)2478291626.46457997.7%
P. nyererei(extant sp.)2347371931.69271996.9%
Platyfish(extant sp.)2375351465.510201499.9%
Red-bellied piranha(extant sp.)26675165015.341149494.4%
Sailfin molly(extant sp.)2361729537.611125294.7%
Sheepshead minnow(extant sp.)22993177212.62258597.5%
Shortfin molly(extant sp.)2404329457.712131994.5%
Spiny chromis(extant sp.)2401626318.414189892.1%
Spotted gar(extant sp.)1834118696.877333298.2%
Stickleback(extant sp.)2078726178.586929998.6%
Swamp eel(extant sp.)2212165033.38450897.7%
Tetraodon(extant sp.)1960227726.07670100.0%
Tiger tail seahorse(extant sp.)2085044645.69051897.5%
Tilapia(extant sp.)2143761334.28846897.8%
Tongue sole(extant sp.)2137174284.695530998.6%
Turbot(extant sp.)2099722954.49440100.0%
Western mosquitofish(extant sp.)2171233963.122933898.4%
Yellowtail amberjack(extant sp.)2472492424.557211691.4%
Zebra mbuna(extant sp.)2715669038.897835798.7%
Zebrafish(extant sp.)3014082336.394328899.0%
Zig-zag eel(extant sp.)2327969337.110191899.9%
 
Other chordates Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Ciona intestinalis(extant sp.)1667148433.981624998.5%
Ciona savignyi(extant sp.)1161628540.61435999.5%
Coelacanth(extant sp.)1956925107.211146492.5%
Hagfish(extant sp.)16513132812.31919698.8%
Lamprey(extant sp.)1041518443.64382663.3%
 
Other eukaryotes Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Caenorhabditis elegans(extant sp.)2022272888.933050100.0%
Fruitfly(extant sp.)1393191547.627313100.0%
Yeast(extant sp.)660017388.25050100.0%
 
Ancestors in Primates Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Catarrhini~30 My26099179119.8862466282.1%
Cebidae~19 My22300159120.1623320285.6%
Cercopithecidae~19 My25910212103.3839400484.5%
Cercopithecinae~13 My2621924692.4985347786.7%
Colobinae~14 My2319847743.1140265388.6%
Haplorrhini~57 My22961159119.7687392282.9%
Hominidae~16 My24277187112.9816315787.0%
Hominoidea~25 My24719189112.8833339486.3%
Homo/Pan group~5 My23579179118.7843233290.1%
Homo/Pan/Gorilla group~9 My24222178120.5835276988.6%
Lemuriformes~37 My18541172100.1287132892.8%
Macaca~5 My24094157139.8946213891.1%
Pan~3 My22913137155.8830156493.2%
Platyrrhini~19 My22727157122.3541352084.5%
Primates~83 My23402124155.6720410682.5%
Rhinopithecus~3 My22186107918.542224289.9%
Simiiformes~45 My24448168118.1747461181.1%
Strepsirrhini~69 My20071153120.0545170891.5%
 
Ancestors in Rodents etc. Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Bathyergidae~33 My1954229260.5190188090.4%
Cavia~4 My1813731454.818394194.8%
Cricetidae~20 My21150134141.9589214089.9%
Cricetidae_B~18 My1944422780.0255129593.3%
Cricetinae~17 My20514148127.5585164692.0%
Cricetulus griseus(extant sp.)2101225876.1277137693.5%
Glires~81 My22568135140.5776360184.0%
Heterocephalus glaber(extant sp.)2150462630.798231589.2%
Hystricognathi~42 My2077319294.6342260287.5%
Hystricomorpha~35 My19877171104.0311209389.5%
Hystricomorpha_A~32 My1884320683.9199156191.7%
Lagomorpha~48 My1844970723.6132175790.5%
Murinae~20 My20884156123.7654159092.4%
Muroidea~44 My22126152126.7682287387.0%
Mus~7 My20733105184.9969131593.7%
Mus_A~6 My20977109180.9972125894.0%
Mus_B~2 My2097795209.1952111094.7%
Myomorpha~51 My21124163113.6465260587.7%
Rodentia~80 My22322133141.8668346084.5%
Sciurognathi~79 My21600129144.9614290886.5%
 
Ancestors in Laurasiatherias Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Bovidae~25 My2151819698.6587218789.8%
Caniformia~44 My20306141131.7518173291.5%
Caniformia_b~44 My1962940245.5131134493.2%
Caprinae~9 My2156920296.2609213590.1%
Carnivora~56 My21409110173.0835237888.9%
Cetartiodactyla~61 My22013169114.2701271487.7%
Chiroptera~60 My18737109515.536177590.5%
Felidae~15 My2024994200.4665140893.0%
Insectivora~68 My1587125942.73886244.2%
Laurasiatheria~88 My24098137144.2980434982.0%
Panthera~7 My19703186100.3366103994.7%
 
Ancestors in mammals Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Afrotheria~94 My1972741442.5122213489.2%
Atlantogenata~100 My2120235352.3230274787.0%
Boreoeutheria~95 My25413143138.31049563077.8%
Diprotodontia~65 My1846618128.214363280.3%
Euarchontoglires~90 My24965139141.9876524579.0%
Eutheria~102 My2405123879.3768516978.5%
Mammalia~184 My2112067324.0107497076.5%
Marsupialia~148 My1966354131.4116266186.5%
Theria~166 My2181730257.3297450879.3%
Xenarthra~64 My1906220717.712312083.6%
 
Ancestors in fish Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Acanthomorphata~148 My28846127316.556784872.8%
Amphiprion~3 My2391843250.8170195991.8%
Anabantaria~81 My23975185117.2877229190.4%
Atherinomorphae~93 My2834331371.4781600578.8%
Carangaria~83 My25162216101.6832320687.3%
Characiphysae~150 My2454764732.399366585.1%
Characoidei~110 My2430180426.272323186.7%
Cichlidae~95 My2673341154.8631420684.3%
Clupeocephala~229 My29629128916.442851371.3%
Cyprinodontiformes~74 My2714035662.2769499281.6%
Cyprinodontoidei~57 My2751135962.5790505681.6%
Eupecaria_A~110 My2323244647.0389227890.2%
Eupercaria~110 My2563824887.7812388284.9%
Euteleosteomorpha~206 My28965102220.963764573.6%
Haplochromini~6 My2793749447.6652440884.2%
NAME_10~22 My2768145051.7755443384.0%
NAME_11~6 My2785546351.0611425484.7%
NAME_12~5 My2775947849.9606390185.9%
NAME_13~67 My2456043949.6231277888.7%
NAME_14~128 My26671193116.6915416684.4%
NAME_3~128 My3124825889.9956805174.2%
NAME_4~57 My2365972129.494248389.5%
NAME_5~42 My2503127480.4769299788.0%
NAME_6~40 My2630083527.398353186.6%
NAME_7~40 My2532691224.678286588.7%
NAME_8(extant sp.)23773164128.1874277188.3%
NAME_9~128 My2805128879.0849530381.1%
Oryzias latipes~2 My24360203104.2825320486.8%
Oryzias~10 My2388830668.2574301987.4%
Otophysi~152 My25093103820.147422583.2%
Ovalentaria~111 My3097927086.3972766775.3%
Percomorphaceae~128 My2960490424.0144789873.3%
Percomorphaceae_A~128 My2975655739.4493778973.8%
Percomorphaceae_B~128 My3111131073.5875831673.3%
Pleuronectoidei~64 My2226431166.7355151893.2%
Poecilia~40 My2654236662.0668385085.5%
Poeciliinae~42 My2752832370.7915469582.9%
Pomacentridae~67 My2515240753.9256320187.3%
Pseudocrenilabrinae~22 My2733943352.8660446083.7%
Seriola~10 My2389631669.1298205691.4%
Synbranchiformes~73 My22616197106.8714157793.0%
Tetraodontidae~51 My2077952935.0400227589.1%
Tetraodontiformes~77 My2277828471.8617239089.5%
Xiphophorus~2 My2421025884.4766244189.9%
 
Ancestors in vertebrates Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Amniota~326 My2194747434.7272550774.9%
Archelosauria~250 My1842341537.5254284884.5%
Chordata~550 My98321452.1295313.1%
Ciona~100 My1104414103.33642341.8%
Cyclostomata~470 My1358112232.421069521.3%
Euteleostomi~420 My2352822746.310924060.7%
Galliformes~45 My1591021667.0346143991.0%
Galloanserae~81 My1674226855.2322194288.4%
Neognathae~105 My1726424261.4344241386.0%
Neopterygii~314 My24028124913.233748868.8%
Osteoglossiformes~163 My23802107719.447295287.6%
Osteoglossocephalai~267 My27713122615.753842569.6%
Passeriformes~45 My1556624257.7269160089.7%
Sarcopterygii~400 My2176315859.820626571.2%
Sauria~267 My1938248133.6237324383.3%
Tetrapoda~359 My21282109614.335565473.4%
Vertebrata~550 My1538210652.421286616.4%
 
Other ancestors Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Bilateria~580 My7279582.1271591.6%
Ecdysozoa~580 My7360432.1272701.2%
Fungi/Metazoa group~1500 My2302242.0222532.1%