Genomicus v89.02 Title
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DYOGEN group

web-code version: 2017-06-13
database version: 89.02
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Statistics on modern & ancestral genomes


Genomicus 89.02 contains 1286709 genes from 70 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 1154508 ancestral genes from 60 ancestral species, grouped into 33680 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.)2213024590.08957099.7%
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
(%)
spretus(extant sp.)1990720995.410650100.0%
Mouse(extant sp.)2214668325.511089100.0%
Rat(extant sp.)2224555403.013117899.6%
Kangaroo rat(extant sp.)1579831242.93671657.5%
Rabbit(extant sp.)1929358132.467847297.6%
Tree shrew(extant sp.)1547131623.34508767.1%
Guinea pig(extant sp.)1867327667.32159799.5%
Squirrel(extant sp.)1882651636.08724998.7%
Pika(extant sp.)1600630103.94439772.5%
 
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.)2160546144.9122490695.8%
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.)2565899256.999422599.1%
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 My22104153127.8787255088.5%
Primates~83 My21790131145.1704278187.2%
Haplorrhini~57 My21335163115.3485254488.1%
Simiiformes~45 My22025147130.4661286287.0%
Catarrhini~31 My22788146135.2870304386.6%
Hominidae~16 My22730153130.6763274387.9%
Homo/Pan group~5 My2035593206.5771114994.4%
Hominoidea~25 My22255147134.5682247888.9%
Homo/Pan/Gorilla group~9 My22172134148.2812231389.6%
Strepsirrhini~69 My1919225370.9198126293.4%
 
Ancestors in Rodents etc. Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Murinae~37 My2032919298.7487138793.2%
Mus~10 My2061776256.2999114394.5%
Rodentia~80 My20267160116.1496169691.6%
Lagomorpha~48 My1834172423.0118168990.8%
Sciurognathi~79 My2011218699.4459161792.0%
Glires~81 My20818155121.1663205290.1%
 
Ancestors in Laurasiatherias Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Insectivora~68 My1577226432.73869544.9%
Bovidae~30 My20393176106.8474159392.2%
Carnivora~56 My20605124150.9654189590.8%
Caniformia~44 My20210138134.4593165891.8%
Chiroptera~60 My18648115014.735168890.9%
Caniformia_b~44 My1961439046.9133132593.2%
Cetartiodactyla~61 My2122920791.2368235288.9%
Laurasiatheria~88 My22900137141.5965352184.6%
 
Ancestors in mammals Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Theria~166 My2084934749.8339357482.9%
Euarchontoglires~90 My22681118163.5805338785.1%
Diprotodontia~65 My1842017818.414346681.2%
Boreoeutheria~95 My23456148130.7939410782.5%
Marsupialia~148 My1952254031.5120250287.2%
Eutheria~102 My2290622583.4644413082.0%
Mammalia~184 My2031066424.5100407479.9%
Xenarthra~64 My1894421087.612282685.1%
Atlantogenata~100 My2080033654.7234241488.4%
Afrotheria~94 My1948740143.7138194490.0%
 
Ancestors in fish Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Poeciliinae~100 My2177762331.7132201890.7%
Atherinomorphae~100 My2183043944.5502228189.6%
Percomorphaceae~125 My2293240449.2602307086.6%
Tetraodontidae~70 My1918962027.4356220888.5%
Ovalentaria~103 My2237135555.9628252288.7%
Clupeocephala~300 My2317620169.217466579.9%
Acanthomorphata~165 My22683164311.427388382.9%
Eupercaria~125 My2106743443.7378210290.0%
Otophysi~150 My22669163012.023318486.0%
 
Ancestors in vertebrates Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Euteleostomi~420 My1993922786.19612769.3%
Galloanserae~81 My1649926356.2331170689.7%
Passeriformes~45 My1558624557.3300154190.1%
Craniata~550 My134855532.22122519.2%
Neopterygii~330 My19942146610.622435578.2%
Olfactores~550 My101581622.1298153.4%
Ciona~100 My1088015363.44564448.1%
Galliformes~45 My1578019673.8384132291.6%
Sauria~267 My1867546234.7316265885.8%
Neognathae~105 My1687624061.8402203987.9%
Amniota~326 My2031843937.0254405880.0%
Sarcopterygii~400 My19657150610.020453476.9%
Archelosauria~250 My1782438740.0259234986.8%
Tetrapoda~359 My1947399115.540409079.0%
 
Other ancestors Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Bilateria~580 My8042672.1279001.8%
Fungi/Metazoa group~1500 My2219252.0221682.3%
Ecdysozoa~580 My7485542.1273691.5%