Genomicus v96.01 Title
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DYOGEN group

web-code version: 2017-06-13
database version: 96.01
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Statistics on modern & ancestral genomes


Genomicus 96.01 contains 3726082 genes from 188 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 3672255 ancestral genes from 162 ancestral species, grouped into 71286 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%
Gelada(extant sp.)2236072306.0115832998.5%
Gibbon(extant sp.)20648108189.182122498.9%
Golden snub-nosed monkey(extant sp.)21132176311.42098695.3%
Gorilla(extant sp.)2158754394.8100426698.8%
Greater bamboo lemur(extant sp.)20277133914.52784595.8%
Human(extant sp.)2244926385.18797699.7%
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%
Ugandan red Colobus(extant sp.)2444368231.7102284288.4%
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
(%)
Alpin marmot(extant sp.)2035020398.725032498.4%
American beaver(extant sp.)2060032915.47296585.6%
Arctic ground squirrel(extant sp.)1964096520.03934398.3%
Brazilian-Guinea pig(extant sp.)1421823560.41823599.8%
Chinese hamster CHOK1GS(extant sp.)20824130159.160614699.3%
Chinese hamster Crigri-PICR(extant sp.)2197237358.219325498.8%
Cricetulus griseus Crigri(extant sp.)1961719979.316113494.2%
Damara mole rat(extant sp.)1773072824.15020298.9%
Daurian ground squirrel(extant sp.)21010163112.32387895.8%
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%
Mongolian gerbil(extant sp.)2111626327.313197490.7%
Mouse(extant sp.)2229294237.0110510100.0%
Naked mole-rat female(extant sp.)2077427475.51589299.6%
Naked mole-rat male(extant sp.)20742196510.21871496.6%
Northern American deer mouse(extant sp.)2164485251.1117130398.6%
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%
Steppe mouse(extant sp.)22907157713.729134294.1%
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%
American bison(extant sp.)2022472726.272115894.3%
American black bear(extant sp.)2054238854.25437678.7%
American mink(extant sp.)1959966928.97023598.8%
Cat(extant sp.)1940962311.910876999.6%
Common shrew(extant sp.)1318719652.73794639.7%
Cow(extant sp.)2186162351.58456699.7%
Dingo(extant sp.)21307155136.240819399.1%
Dog(extant sp.)1985781243.360615299.2%
Dolphin(extant sp.)1655031794.45247285.1%
Donkey(extant sp.)1992241047.913628898.6%
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.)21516129165.576517099.2%
Megabat(extant sp.)1699031874.35319881.2%
Microbat(extant sp.)19728124914.939116994.1%
Pig(extant sp.)22342194114.5128212799.4%
Polar bear(extant sp.)1869933855.011612099.4%
Red fox(extant sp.)2026635756.311717099.2%
Sheep(extant sp.)20921117174.087056497.3%
Tiger(extant sp.)1754450634.5626299.6%
Wild yak(extant sp.)2083221389.31588395.8%
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%
koala(extant sp.)1983246042.79719299.0%
 
Birds & Reptiles Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Abingdon island giant tortoise(extant sp.)2020020399.61571596.5%
Agassiz s desert tortoise(extant sp.)2013543003.74421179.1%
Argentine black and white tegu(extant sp.)1933822684.920115599.2%
Australian saltwater crocodile(extant sp.)1522670217.53920100.0%
Bengalese finch(extant sp.)1591773921.24327998.2%
Blue tit(extant sp.)1547033541.2212165989.3%
Blue-crowned manakin(extant sp.)1532048331.16630398.0%
Budgerigar(extant sp.)1456843731.512880294.5%
Central bearded dragon(extant sp.)19580118416.03160196.9%
Chicken(extant sp.)1677949341.85463299.8%
Chilean tinamou(extant sp.)1570457526.95426298.3%
Chinese turtle(extant sp.)18189146711.92372696.0%
Common canary(extant sp.)1522524160.032375395.1%
Dark-eyed junco(extant sp.)1455163226.851626398.2%
Duck(extant sp.)1661631845.4478217186.9%
Emu(extant sp.)1561577619.83928798.2%
Flycatcher(extant sp.)1530349130.59233497.8%
Golden-collared manakin(extant sp.)1592835940.9225123492.3%
Great Tit(extant sp.)15003146101.451219698.7%
Great spotted kiwi(extant sp.)16674129612.52351396.9%
Helmeted guineafowl(extant sp.)1566117687.572926798.3%
Japanese quail(extant sp.)1573216693.452722598.6%
Little spotted kiwi(extant sp.)16196107714.52755396.6%
Lizard(extant sp.)18595105516.3868137092.6%
Mainland tiger snake(extant sp.)1896486719.763188390.1%
Okarito brown kiwi(extant sp.)16257106014.93043597.3%
Pink-footed goose(extant sp.)1554459125.86228398.2%
Ruff(extant sp.)1642153130.411329498.2%
Spoon-billed sandpiper(extant sp.)1633196315.93898894.0%
Turkey(extant sp.)1412314097.250551096.4%
White-throated sparrow(extant sp.)1386260122.35844296.8%
Zebra finch(extant sp.)1748868257.27121100.0%
painted turtle(extant sp.)2117691022.158104795.1%
tuatara(extant sp.)17628142212.11947397.3%
 
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 My2832023295.0862627377.8%
Cebidae~19 My22574177108.5608337385.1%
Cercopithecidae~19 My2855526486.8894564480.2%
Cercopithecinae~13 My2814425891.61020449984.0%
Colobinae~14 My2684836260.7261486581.9%
Haplorrhini~57 My24975164119.5715538578.4%
Hominidae~16 My25002202105.5816370085.2%
Hominoidea~25 My25396215100.3866382384.9%
Homo/Pan group~5 My23773180118.6868241889.8%
Homo/Pan/Gorilla group~9 My24461188114.9936286588.3%
Lemuriformes~37 My2101223081.3378232388.9%
Macaca~5 My24398153144.4950230090.6%
Pan~3 My23037134159.8693162792.9%
Platyrrhini~19 My23051172112.3584373983.8%
Primates~83 My25786155129.1887578377.6%
Rhinopithecus~3 My22389106818.843234389.5%
Simiiformes~45 My26523193105.5774616776.7%
Strepsirrhini~69 My21453173109.5672250288.3%
 
Ancestors in Rodents etc. Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Bathyergidae~33 My1968728861.4192200289.8%
Castorimorpha~63 My1987636042.888445877.6%
Cavia~4 My1816531255.218294694.8%
Cricetidae~20 My22689164119.9679302686.7%
Cricetidae_B~18 My20838161118.8532171391.8%
Cricetinae~17 My21786176110.3749238089.1%
Cricetulus griseus(extant sp.)2271021096.9540236589.6%
Cricetulus griseus_a(extant sp.)2140721892.3369127794.0%
Glires~81 My25426177111.0805578177.3%
Heterocephalus glaber(extant sp.)2162661631.397234489.2%
Hystricomorpha~42 My2112219892.0357290286.3%
Hystricomorpha_a~35 My20031177100.7300220989.0%
Hystricomorpha_b~32 My1894020385.4205161091.5%
Lagomorpha~48 My1856670923.6127185390.0%
Marmotini~11 My2280931662.3340312286.3%
Marmotini_b~11 My2234946342.4150272587.8%
Marmotini_c~11 My2166670927.571220289.8%
Muridae~29 My23941182109.1852408083.0%
Murinae~20 My22035176111.9650233989.4%
Muroidea~44 My2293922385.8394379783.4%
Mus~7 My22217151132.0978228589.7%
Mus_A~6 My22613150134.91033238589.5%
Mus_B~2 My23310155132.8960273388.3%
Mus_C~2 My22706151134.1802246089.2%
Myomorpha~51 My2290420194.6487389783.0%
Rodentia~80 My25415190103.4698577377.3%
Sciurognathi~79 My25121196100.2689548078.2%
 
Ancestors in Laurasiatherias Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Bos~4 My2248024583.6393200791.1%
Bovidae~25 My2366123884.5689354485.0%
Bovinae~5 My2304624384.1508260988.7%
Canidae~14 My22031172112.4393270387.7%
Caniformia~44 My23917168118.0681408982.9%
Caniformia_b~44 My2307223583.6433342785.1%
Canis lupus~1 My21440147131.5517210990.2%
Caprinae~9 My2184421790.5593220689.9%
Carnivora~56 My24144143139.1878425182.4%
Cetartiodactyla~61 My23466190104.1668369084.3%
Chiroptera~60 My18847110315.437183090.3%
Equus~7 My2094321591.1337134793.6%
Felidae~15 My2043388215.5655147292.8%
Insectivora~68 My1593326182.73887444.3%
Laurasiatheria~88 My27150190109.21105640476.4%
Mustelinae~8 My2036734155.1161159092.2%
Panthera~7 My19804182102.9350108294.5%
Ursidae~23 My2199439049.5155267187.9%
Ursus~6 My2109349038.6110220289.6%
 
Ancestors in mammals Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Afrotheria~94 My1990140743.3125227988.5%
Atlantogenata~100 My2164433355.7242308285.8%
Boreoeutheria~95 My28977190108.91085828771.4%
Diprotodontia~35 My1916754631.166219188.6%
Euarchontoglires~90 My28396191107.4877787672.3%
Eutheria~102 My2667026374.0738720973.0%
Mammalia~184 My2375366025.8122670771.8%
Marsupialia~85 My2089725769.8469297085.8%
Marsupialia_b~85 My2037243141.2120263587.1%
Theria~166 My2453530559.4407641973.8%
Xenarthra~64 My1925120897.712317483.5%
 
Ancestors in fish Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Acanthomorphata~148 My30280126116.857907670.0%
Amphiprion~3 My2399444049.9172202191.6%
Anabantaria~81 My24225201108.3856245089.9%
Atherinomorphae~93 My2921536062.5781671477.0%
Carangaria~83 My2555823295.1840348786.4%
Characiphysae~150 My2482566731.492385984.5%
Characoidei~110 My2447280626.268335386.3%
Cichlidae~95 My2717540256.0724464382.9%
Clupeocephala~229 My31334135215.842990768.4%
Cyprinodontiformes~74 My2783938757.5746557980.0%
Cyprinodontoidei~57 My2816039457.4701556380.2%
Eupecaria_A~110 My2343845546.2363240189.8%
Eupercaria~110 My2629028876.1762437983.3%
Euteleosteomorpha~206 My30473105120.566892070.7%
Haplochromini~6 My2813148048.9615465183.5%
NAME_10~22 My2837046949.8708503682.2%
NAME_11~6 My2797146450.8568439784.3%
NAME_12~5 My2779845452.4535398985.7%
NAME_13~67 My2472744149.5245290688.2%
NAME_14~128 My2732024393.3912464883.0%
NAME_3~128 My3277633071.3917925471.8%
NAME_4~57 My2385872529.293267388.8%
NAME_5~42 My2517128178.4799313087.6%
NAME_6~40 My2641883227.4104363486.2%
NAME_7~40 My2541989225.180300788.2%
NAME_8(extant sp.)23852173121.6871282388.2%
NAME_9~128 My2880533069.4849590379.5%
Neopterygii~314 My25690126913.334884265.6%
Oryzias latipes~2 My24437202104.8818327686.6%
Oryzias~10 My2402429371.1516318086.8%
Osteoglossiformes~163 My24029105919.846308287.2%
Osteoglossocephalai~267 My29447128215.355980266.7%
Otophysi~152 My25499106619.645457782.1%
Ovalentaria~111 My3223032073.6933868773.0%
Percomorphaceae~128 My3114293423.5141915370.6%
Percomorphaceae_A~128 My3127059237.6537902271.1%
Percomorphaceae_B~128 My3271637362.0874958570.7%
Pleuronectoidei~64 My2243931366.4333166492.6%
Poecilia~40 My2669236662.0634400285.0%
Poeciliinae~42 My2798033668.1870511181.7%
Pomacentridae~67 My2538942252.1290340186.6%
Pseudocrenilabrinae~22 My2781046849.1712483282.6%
Seriola~10 My2406631768.9293221190.8%
Synbranchiformes~73 My22773202104.3743169792.5%
Tetraodontidae~51 My2086253034.9402234788.7%
Tetraodontiformes~77 My2301530167.8615259588.7%
Xiphophorus~2 My2427524887.8729249289.7%
 
Ancestors in Birds Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Anatidae~30 My1660227355.2255153690.7%
Apteryx~10 My1741270622.354168590.3%
Apteryx_b~10 My1689988017.635143591.5%
Aves~111 My2218029857.2502512376.9%
Calidris~10 My1663232846.6235135391.9%
Estrildinae~10 My1707625459.1398206887.9%
Galliformes~46 My1762718484.6514205888.3%
Galloanserae~80 My1861522272.2522259086.1%
Neognathae~105 My2160527162.0545479877.8%
Neognathae_b~105 My2038325564.4469397180.5%
Neognathae_c~105 My1712424064.2368172289.9%
Palaeognathae~62 My1828233348.5227214488.3%
Palaeognathae_b~62 My1767242037.8100178389.9%
Paridae~13 My1610816887.0426149290.7%
Passerellidae~5 My1575918876.5338138491.2%
Passeriformes~65 My1948024066.3529355981.7%
Passeriformes_b~65 My1944824564.9523354581.8%
Passeriformes_c~65 My1709219876.0513204788.0%
Passeriformes_d~65 My1902426060.5457329082.7%
Passeroidea~35 My1799625460.6398259785.6%
Phasianidae~42 My1719516394.7510175389.8%
Phasianidae_b~42 My1620515497.0504126192.2%
Pipridae~6 My1592322166.4270123992.2%
 
Ancestors in vertebrates Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Amniota~326 My2649551534.4311876566.9%
Archelosauria~250 My2471537548.8394640474.1%
Archosauria~236 My2219532252.9439516876.7%
Chordata~550 My103361612.1299963.3%
Ciona~100 My1108514183.33643841.9%
Cryptodira~161 My2144955432.1124365383.0%
Cyclostomata~470 My1372012412.321081121.2%
Episquamata~178 My2106928361.6598365082.7%
Euteleostomi~420 My2562623066.4101087657.6%
Iguania~157 My1922249633.999238687.6%
Lepidosauria~251 My2140641941.7261392481.7%
Sarcopterygii~400 My24113160410.021811666.3%
Sauria~267 My2559637748.6437726271.6%
Testudinidae~53 My2113318879.316363682.8%
Testudinoidea~80 My2195575723.980385582.4%
Tetrapoda~359 My23777110214.739761268.0%
Toxicofera~168 My2053435049.2308330183.9%
Vertebrata~550 My1620510852.321366515.7%
 
Other ancestors Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Bilateria~580 My7548692.1274061.9%
Ecdysozoa~580 My7438532.1273291.5%
Fungi/Metazoa group~1500 My2396322.1223302.8%