Genomicus v88.01 Title
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DYOGEN group

web-code version: 2014-09-19
database version: 88.01


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Statistics on modern & ancestral genomes


Genomicus 88.01 contains 1286730 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 1150924 ancestral genes from 60 ancestral species, grouped into 33422 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.)2216768325.911089100.0%
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%
Tasmanian harrisii(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
(%)
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 My22023132147.9780249788.7%
Primates~83 My21706113167.9697273587.4%
Haplorrhini~57 My21244151124.3535247988.3%
Simiiformes~45 My21955143133.7664283587.1%
Catarrhini~31 My22744117168.5860302986.7%
Hominidae~16 My22660145137.8760267488.2%
Homo/Pan group~5 My2035197198.2772112294.5%
Hominoidea~25 My22193142139.3741241689.1%
Homo/Pan/Gorilla group~9 My22136135147.3816225389.8%
Strepsirrhini~69 My1919324772.6238126993.4%
 
Ancestors in Rodents etc. Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Murinae~37 My20264185102.1486136893.2%
Mus~10 My2060669282.2998113294.5%
Rodentia~80 My20162159116.5493164591.8%
Lagomorpha~48 My1833571723.2119168590.8%
Sciurognathi~79 My19992175105.4465155392.2%
Glires~81 My20716137136.8705197890.5%
 
Ancestors in Laurasiatherias Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Insectivora~68 My1576426442.73868744.9%
Bovidae~30 My20369168111.9542156992.3%
Carnivora~56 My20625111168.3628194390.6%
Caniformia~44 My20255134138.4566171491.5%
Chiroptera~60 My18624114714.836166591.1%
Caniformia_b~44 My1963339845.9129136893.0%
Cetartiodactyla~61 My2126021289.0365238488.8%
Laurasiatheria~88 My22889117165.3968355184.5%
 
Ancestors in mammals Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Theria~166 My2069133850.9337349583.1%
Euarchontoglires~90 My22489106181.4844326485.5%
Diprotodontia~65 My1836417858.414345781.2%
Boreoeutheria~95 My23298119162.0956401682.8%
Marsupialia~148 My1940952732.2112246487.3%
Eutheria~102 My2275021985.4623404482.2%
Mammalia~184 My2014066024.692393480.5%
Xenarthra~64 My1895021027.712282785.1%
Atlantogenata~100 My2075134253.7233238288.5%
Afrotheria~94 My1940139544.3137189290.2%
 
Ancestors in fish Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Poeciliinae~100 My2174362531.6137196591.0%
Atherinomorphae~100 My2178646042.5501222589.8%
Percomorphaceae~125 My2285341148.3648301786.8%
Tetraodontidae~70 My1918962827.1351218988.6%
Ovalentaria~103 My2231737353.2524248088.9%
Clupeocephala~300 My2310120449.117456680.2%
Acanthomorphata~165 My22592163011.527383283.0%
Eupercaria~125 My2100641945.2391205590.2%
Otophysi~150 My22609163211.924315086.1%
 
Ancestors in vertebrates Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Euteleostomi~420 My1976622836.19592370.0%
Galloanserae~81 My1644225757.5353165889.9%
Passeriformes~45 My1552624258.1296147290.5%
Vertebrata~550 My133915492.32121549.2%
Neopterygii~330 My19886145510.723433778.2%
Olfactores~550 My101491662.1297933.5%
Ciona~100 My1084715433.44556748.7%
Galliformes~45 My1572519474.5368127991.9%
Sauria~267 My1864443037.1317268285.6%
Neognathae~105 My1679323363.5397199688.1%
Amniota~326 My2020543537.3273397280.3%
Sarcopterygii~400 My19512150710.020439677.5%
Archelosauria~250 My1776837341.4251234286.8%
Tetrapoda~359 My19342100115.441395879.5%
 
Other ancestors Age Genes Blocks Average size
(nb genes)
N50 size
(nb genes)
Genes not
in blocks
Coverage
(%)
Bilateria~580 My8070652.1279331.7%
Fungi/Metazoa group~1500 My2221262.0221682.4%
Ecdysozoa~580 My7499532.2273851.5%