Genomicus v90.01 Title
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DYOGEN group

web-code version: 2017-06-13
database version: 90.01
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Statistics on modern & ancestral genomes


Genomicus 90.01 contains 1613382 genes from 87 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 1399291 ancestral genes from 72 ancestral species, grouped into 35888 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
(%)
Human(extant sp.)2214324590.18967099.7%
Olive baboon(extant sp.)19210109173.8101226298.6%
Orangutan(extant sp.)2042453385.48430100.0%
Rhesus(extant sp.)2109958356.9111840098.1%
Gorilla(extant sp.)2096227776.410160100.0%
Gibbon(extant sp.)1857539446.512626898.6%
Tarsier(extant sp.)1362815402.321015025.5%
Mouse lemur(extant sp.)1810389420.04323298.7%
Vervet Monkey(extant sp.)1916554353.76966599.7%
Bushbaby(extant sp.)1950637451.811515199.2%
Marmoset(extant sp.)20978123166.1106154397.4%
Chimpanzee(extant sp.)1875961304.480319299.0%
 
Rodents etc. Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Chinese hamster Crigri(extant sp.)1961719979.316113494.2%
Degu(extant sp.)1998239650.111313099.3%
Naked mole-rat female(extant sp.)2077427475.51589299.6%
Rat(extant sp.)2224555403.013117899.6%
Kangaroo rat(extant sp.)1691128957.710823998.6%
Shrew mouse(extant sp.)1906224794.29250100.0%
Prairie vole(extant sp.)1913019299.14849799.5%
Pika(extant sp.)1600630103.94439772.5%
Ryukyu mouse(extant sp.)1921020960.59650100.0%
Squirrel(extant sp.)1847448637.69021298.9%
Chinese hamster CHOK1GS(extant sp.)20824130159.160614699.3%
Upper Galilee mountains blind mole rat(extant sp.)18647107917.03035498.1%
Mouse(extant sp.)2214368325.511089100.0%
Tree shrew(extant sp.)1547131623.34508767.1%
Northern American deer mouse(extant sp.)19854102519.03939998.0%
Naked mole-rat male(extant sp.)20742196510.21871496.6%
Long-tailed chinchilla(extant sp.)1780921283.71546999.6%
spretus(extant sp.)1947720973.910450100.0%
Golden Hamster(extant sp.)1825731257.011046597.5%
Brazilian-Guinea pig(extant sp.)1421823560.41823599.8%
Lesser Egyptian jerboa(extant sp.)1784523874.71287799.6%
Rabbit(extant sp.)1929358132.467847297.6%
Guinea pig(extant sp.)1809525869.92146199.7%
Damara mole rat(extant sp.)1773072824.15020298.9%
 
Laurasiatherias Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Hedgehog(extant sp.)1460121052.42960634.2%
Microbat(extant sp.)19728124914.939116994.1%
Pig(extant sp.)22342194114.5128212799.4%
Horse(extant sp.)2044960340.17504699.8%
Cat(extant sp.)1949342459.8109118399.1%
Sheep(extant sp.)20921117174.087056497.3%
Dog(extant sp.)1985681243.360615299.2%
Cow(extant sp.)1999432624.57791199.9%
Dolphin(extant sp.)1655031794.45247285.1%
Alpaca(extant sp.)1176520064.45299974.5%
Giant Panda(extant sp.)19343181910.21879995.9%
Ferret(extant sp.)1991050339.09627698.6%
Megabat(extant sp.)1699031874.35319881.2%
Common shrew(extant sp.)1318719652.73794639.7%
 
Xenarthras etc. Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Sloth(extant sp.)1239311812.22977821.1%
Armadillo(extant sp.)2271125548.313144893.6%
 
Afrotherias etc. Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Hyrax(extant sp.)1605728342.93778351.5%
Elephant(extant sp.)2003335555.823022898.9%
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%
Wallaby(extant sp.)1529017202.421111927.3%
Tasmanian harrisii(extant sp.)1878819668.715165491.2%
 
Birds & Reptiles Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Turkey(extant sp.)1412314097.250551096.4%
Duck(extant sp.)15634138110.517113592.7%
Lizard(extant sp.)18595105516.3868137092.6%
Chinese turtle(extant sp.)18189146711.92372696.0%
Chicken(extant sp.)1834651033.3517138792.4%
Zebra finch(extant sp.)1748868257.27121100.0%
Flycatcher(extant sp.)1530349130.59233497.8%
 
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
(%)
Tetraodon(extant sp.)1960227726.07670100.0%
Spotted gar(extant sp.)1834118696.877333298.2%
Amazon molly(extant sp.)2361599723.25250997.8%
Atlantic cod(extant sp.)2009527166.410266386.7%
Zebrafish(extant sp.)25728103247.7100422099.1%
Medaka(extant sp.)1969933157.874155697.2%
Tilapia(extant sp.)2143761334.28846897.8%
Fugu(extant sp.)1852385320.552107794.2%
Cave fish(extant sp.)23042136715.937127794.5%
Stickleback(extant sp.)2078726178.586929998.6%
Platyfish(extant sp.)20379124415.444121894.0%
 
Other chordates Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Ciona savignyi(extant sp.)1161628540.61435999.5%
Lamprey(extant sp.)1041518443.64382663.3%
Coelacanth(extant sp.)1956925107.211146492.5%
Ciona intestinalis(extant sp.)1667148433.981624998.5%
 
Other eukaryotes Age Genes Contigs Average size
(nb genes)
N50 size
(nb genes)
Genes not
in contigs
Coverage
(%)
Yeast(extant sp.)669217393.65130100.0%
Caenorhabditis elegans(extant sp.)2036272908.933130100.0%
Fruitfly(extant sp.)1391891546.127343100.0%
 
Ancestors in Primates Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Cercopithecinae~11 My22144156125.4765258188.3%
Primates~83 My21913117163.0711284787.0%
Haplorrhini~57 My21430166113.6537257688.0%
Simiiformes~45 My22077164117.1666287787.0%
Catarrhini~31 My22894145136.3854312686.3%
Hominidae~16 My22710174115.1789267688.2%
Homo/Pan group~5 My20415102188.8806115694.3%
Hominoidea~25 My22235150131.8747247088.9%
Homo/Pan/Gorilla group~9 My22205140142.3765227889.7%
Strepsirrhini~69 My1921024274.1194127693.4%
 
Ancestors in Rodents etc. Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Glires~81 My21555128147.0670274187.3%
Myomorpha~51 My20688151122.3466222089.3%
Murinae~20 My20717161119.9641141193.2%
Hystricognathi~42 My2041820787.6351228688.8%
Mus~7 My20736108179.9908130393.7%
Rodentia~80 My21500127147.6617275687.2%
Mus_B~2 My2110295209.11021123794.1%
Cricetidae~20 My20897131145.3576186991.1%
Cavia~4 My1805431654.520482395.4%
Lagomorpha~48 My1827474922.2114164091.0%
Cricetidae_B~18 My1941124773.7238121293.8%
Muroidea~44 My21676134143.6745243488.8%
Mus_A~6 My21055111177.71013132993.7%
Bathyergidae~33 My1950029160.7178184690.5%
Hystricomorpha_A~32 My1872020385.0187147092.1%
Hystricomorpha~10 My19626170104.3315189190.4%
Cricetulus griseus(extant sp.)2096521491.8326132293.7%
Sciurognathi~79 My21041134138.9598242288.5%
Cricetinae~10 My20397143132.0637151792.6%
Heterocephalus glaber(extant sp.)2143760831.6103221789.7%
 
Ancestors in Laurasiatherias Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Insectivora~68 My1576626452.73867845.0%
Bovidae~30 My20363176106.9533155592.4%
Carnivora~56 My20530101184.7663187490.9%
Caniformia~44 My20172131141.4586165091.8%
Chiroptera~60 My18602114114.936165591.1%
Caniformia_b~44 My1957439246.6129132493.2%
Cetartiodactyla~61 My21359189100.9572229889.2%
Laurasiatheria~88 My22807117166.11023337685.2%
 
Ancestors in mammals Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Theria~166 My2077334649.8313353683.0%
Euarchontoglires~90 My23260123157.7855386683.4%
Marsupialia~148 My1943554930.9104245487.4%
Boreoeutheria~95 My23657139139.4936427481.9%
Diprotodontia~65 My1838117868.414345281.2%
Eutheria~102 My2284221487.5645412681.9%
Afrotheria~94 My1944240743.1139188190.3%
Xenarthra~64 My1893420977.712279685.2%
Atlantogenata~100 My2073133554.9234234388.7%
Mammalia~184 My2028667324.1104405580.0%
 
Ancestors in fish Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Poeciliinae~100 My2168763431.1118194291.0%
Atherinomorphae~100 My2178245143.3540225489.7%
Percomorphaceae~125 My2290042746.4597306686.6%
Tetraodontidae~70 My1917563526.8273217688.7%
Ovalentaria~103 My2234437053.6581252988.7%
Clupeocephala~300 My2319320249.117474479.5%
Acanthomorphata~165 My22616164011.427387382.9%
Eupercaria~125 My2103544742.4390210090.0%
Otophysi~150 My22726161912.024331385.4%
 
Ancestors in vertebrates Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Euteleostomi~420 My1985522616.09620268.8%
Neopterygii~330 My19825147010.522443677.6%
Passeriformes~45 My1552824157.9291156389.9%
Vertebrata~550 My135145402.22123058.9%
Sarcopterygii~400 My1961315269.819464276.3%
Chordata~550 My102021662.1298513.4%
Ciona~100 My1088615213.44566648.0%
Galloanserae~81 My1640126555.6324165889.9%
Galliformes~45 My1571321068.6383130091.7%
Sauria~267 My1857545534.9268269585.5%
Neognathae~105 My1678223862.0406203087.9%
Amniota~326 My2029945635.4246415279.5%
Archelosauria~250 My1769439339.1262232586.9%
Tetrapoda~359 My19488102714.838424478.2%
 
Other ancestors Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Bilateria~580 My8153662.2280111.7%
Fungi/Metazoa group~1500 My2268302.0222072.7%
Ecdysozoa~580 My7523532.1274111.5%