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web-code version: 2017-06-13
database version: 91.01
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Genomicus 91.01 contains 1873152 genes from 99 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 1602940 ancestral genes from 80 ancestral species, grouped into 38638 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 (%)
Gorilla	(extant sp.)	21588	54	394.9	1004	266	98.8%
Coquerels sifaka	(extant sp.)	17884	624	28.4	53	184	99.0%
Black snub-nosed monkey	(extant sp.)	20824	1495	13.3	24	1002	95.2%
Crab-eating macaque	(extant sp.)	21404	73	290.5	1154	198	99.1%
Bushbaby	(extant sp.)	19506	374	51.8	115	151	99.2%
Pig-tailed macaque	(extant sp.)	20872	341	60.9	117	100	99.5%
Mas night monkey	(extant sp.)	20320	630	31.8	65	263	98.7%
Gibbon	(extant sp.)	20648	108	189.1	821	224	98.9%
Capuchin	(extant sp.)	20200	832	24.0	51	201	99.0%
Mouse lemur	(extant sp.)	18103	43	420.3	789	29	99.8%
Angola colobus	(extant sp.)	20467	615	33.1	66	114	99.4%
pygmy chimpanzee	(extant sp.)	21041	71	294.2	946	153	99.3%
Human	(extant sp.)	22143	245	90.1	896	70	99.7%
Orangutan	(extant sp.)	20424	53	385.4	843	0	100.0%
Rhesus	(extant sp.)	21099	58	356.9	1118	400	98.1%
Tarsier	(extant sp.)	18304	3258	4.8	6	2616	85.7%
Chimpanzee	(extant sp.)	23302	250	91.8	963	351	98.5%
Golden snub-nosed monkey	(extant sp.)	21132	1763	11.4	20	986	95.3%
Olive baboon	(extant sp.)	21464	131	161.8	1138	269	98.7%
Vervet Monkey	(extant sp.)	19165	54	353.7	696	65	99.7%
Sooty mangabey	(extant sp.)	20746	415	49.7	107	127	99.4%
Drill	(extant sp.)	20660	1214	16.8	31	314	98.5%
Bolivian squirrel monkey	(extant sp.)	19290	267	72.1	146	50	99.7%
Marmoset	(extant sp.)	20978	123	166.1	1061	543	97.4%
Rodents etc.	Age	Genes	Contigs	Average size (nb genes)	N50 size (nb genes)	Genes not in contigs	Coverage (%)
Chinese hamster Crigri	(extant sp.)	19617	1997	9.3	16	1134	94.2%
Ryukyu mouse	(extant sp.)	19210	20	960.5	965	0	100.0%
Naked mole-rat female	(extant sp.)	20774	274	75.5	158	92	99.6%
Rat	(extant sp.)	22245	55	403.0	1311	78	99.6%
Kangaroo rat	(extant sp.)	16911	289	57.7	108	239	98.6%
Shrew mouse	(extant sp.)	19062	24	794.2	925	0	100.0%
Prairie vole	(extant sp.)	19130	192	99.1	484	97	99.5%
Pika	(extant sp.)	16006	3010	3.9	4	4397	72.5%
Degu	(extant sp.)	19982	396	50.1	113	130	99.3%
Squirrel	(extant sp.)	18474	486	37.6	90	212	98.9%
Chinese hamster CHOK1GS	(extant sp.)	20824	130	159.1	606	146	99.3%
Upper Galilee mountains blind mole rat	(extant sp.)	18647	1079	17.0	30	354	98.1%
Mouse	(extant sp.)	22153	68	325.6	1108	9	100.0%
Tree shrew	(extant sp.)	15471	3162	3.3	4	5087	67.1%
Northern American deer mouse	(extant sp.)	19854	1025	19.0	39	399	98.0%
Naked mole-rat male	(extant sp.)	20742	1965	10.2	18	714	96.6%
Long-tailed chinchilla	(extant sp.)	17809	212	83.7	154	69	99.6%
spretus	(extant sp.)	19477	20	973.9	1045	0	100.0%
Golden Hamster	(extant sp.)	18257	312	57.0	110	465	97.5%
Brazilian-Guinea pig	(extant sp.)	14218	235	60.4	182	35	99.8%
Lesser Egyptian jerboa	(extant sp.)	17845	238	74.7	128	77	99.6%
Rabbit	(extant sp.)	19293	581	32.4	678	472	97.6%
Guinea pig	(extant sp.)	18095	258	69.9	214	61	99.7%
Damara mole rat	(extant sp.)	17730	728	24.1	50	202	98.9%
Laurasiatherias	Age	Genes	Contigs	Average size (nb genes)	N50 size (nb genes)	Genes not in contigs	Coverage (%)
Hedgehog	(extant sp.)	14601	2105	2.4	2	9606	34.2%
Microbat	(extant sp.)	19728	1249	14.9	39	1169	94.1%
Pig	(extant sp.)	22342	194	114.5	1282	127	99.4%
Horse	(extant sp.)	20449	60	340.1	750	46	99.8%
Cat	(extant sp.)	20374	35	572.7	1153	329	98.4%
Sheep	(extant sp.)	20921	117	174.0	870	564	97.3%
Dog	(extant sp.)	19856	81	243.3	606	152	99.2%
Cow	(extant sp.)	19994	32	624.5	779	11	99.9%
Dolphin	(extant sp.)	16550	3179	4.4	5	2472	85.1%
Alpaca	(extant sp.)	11765	2006	4.4	5	2999	74.5%
Giant Panda	(extant sp.)	19343	1819	10.2	18	799	95.9%
Ferret	(extant sp.)	19910	503	39.0	96	276	98.6%
Megabat	(extant sp.)	16990	3187	4.3	5	3198	81.2%
Common shrew	(extant sp.)	13187	1965	2.7	3	7946	39.7%
Xenarthras etc.	Age	Genes	Contigs	Average size (nb genes)	N50 size (nb genes)	Genes not in contigs	Coverage (%)
Sloth	(extant sp.)	12393	1181	2.2	2	9778	21.1%
Armadillo	(extant sp.)	22711	2554	8.3	13	1448	93.6%
Afrotherias etc.	Age	Genes	Contigs	Average size (nb genes)	N50 size (nb genes)	Genes not in contigs	Coverage (%)
Hyrax	(extant sp.)	16057	2834	2.9	3	7783	51.5%
Elephant	(extant sp.)	20033	355	55.8	230	228	98.9%
Tenrec	(extant sp.)	16575	2559	2.6	2	10047	39.4%
Marsupials & Monotremes	Age	Genes	Contigs	Average size (nb genes)	N50 size (nb genes)	Genes not in contigs	Coverage (%)
Opossum	(extant sp.)	21327	11	1938.8	2870	0	100.0%
Platypus	(extant sp.)	21698	1855	6.8	22	9138	57.9%
Wallaby	(extant sp.)	15290	1720	2.4	2	11119	27.3%
Tasmanian devil	(extant sp.)	18788	1966	8.7	15	1654	91.2%
Birds & Reptiles	Age	Genes	Contigs	Average size (nb genes)	N50 size (nb genes)	Genes not in contigs	Coverage (%)
Turkey	(extant sp.)	14123	140	97.2	505	510	96.4%
Duck	(extant sp.)	15634	1381	10.5	17	1135	92.7%
Lizard	(extant sp.)	18595	1055	16.3	868	1370	92.6%
Chinese turtle	(extant sp.)	18189	1467	11.9	23	726	96.0%
Chicken	(extant sp.)	18346	510	33.3	517	1387	92.4%
Zebra finch	(extant sp.)	17488	68	257.2	712	1	100.0%
Flycatcher	(extant sp.)	15303	491	30.5	92	334	97.8%
Amphibians	Age	Genes	Contigs	Average size (nb genes)	N50 size (nb genes)	Genes not in contigs	Coverage (%)
Frog	(extant sp.)	18442	1339	13.1	23	902	95.1%
Fish	Age	Genes	Contigs	Average size (nb genes)	N50 size (nb genes)	Genes not in contigs	Coverage (%)
Tetraodon	(extant sp.)	19602	27	726.0	767	0	100.0%
Spotted gar	(extant sp.)	18341	186	96.8	773	332	98.2%
Amazon molly	(extant sp.)	23615	997	23.2	52	509	97.8%
Atlantic cod	(extant sp.)	20095	2716	6.4	10	2663	86.7%
Zebrafish	(extant sp.)	25728	103	247.7	1004	220	99.1%
Medaka	(extant sp.)	19699	331	57.8	741	556	97.2%
Tilapia	(extant sp.)	21437	613	34.2	88	468	97.8%
Fugu	(extant sp.)	18523	853	20.5	52	1077	94.2%
Cave fish	(extant sp.)	23042	1367	15.9	37	1277	94.5%
Stickleback	(extant sp.)	20787	261	78.5	869	299	98.6%
Platyfish	(extant sp.)	20379	1244	15.4	44	1218	94.0%
Other chordates	Age	Genes	Contigs	Average size (nb genes)	N50 size (nb genes)	Genes not in contigs	Coverage (%)
Ciona savignyi	(extant sp.)	11616	285	40.6	143	59	99.5%
Lamprey	(extant sp.)	10415	1844	3.6	4	3826	63.3%
Coelacanth	(extant sp.)	19569	2510	7.2	11	1464	92.5%
Ciona intestinalis	(extant sp.)	16671	484	33.9	816	249	98.5%
Other eukaryotes	Age	Genes	Contigs	Average size (nb genes)	N50 size (nb genes)	Genes not in contigs	Coverage (%)
Yeast	(extant sp.)	6692	17	393.6	513	0	100.0%
Caenorhabditis elegans	(extant sp.)	20222	7	2888.9	3305	0	100.0%
Fruitfly	(extant sp.)	13931	9	1547.6	2731	3	100.0%
Ancestors in Primates	Age	Genes	Blocks	Average size (nb genes)	N50 size (nb genes)	Genes not in blocks	Coverage (%)
Cercopithecinae	~13 My	25941	197	115.6	922	3176	87.8%
Rhinopithecus	~3 My	22085	1048	19.0	45	2146	90.3%
Homo/Pan/Gorilla group	~9 My	24120	176	122.2	821	2608	89.2%
Primates	~83 My	22706	129	149.1	694	3477	84.7%
Haplorrhini	~57 My	22386	147	129.6	520	3334	85.1%
Simiiformes	~45 My	24139	170	117.1	740	4225	82.5%
Catarrhini	~30 My	25684	179	119.8	861	4240	83.5%
Hominidae	~16 My	24184	181	117.0	845	3013	87.5%
Macaca	~5 My	23943	128	171.3	881	2013	91.6%
Lemuriformes	~37 My	18345	191	89.7	261	1205	93.4%
Homo/Pan group	~5 My	23499	187	113.8	947	2222	90.5%
Hominoidea	~25 My	24593	175	122.0	821	3242	86.8%
Platyrrhini	~19 My	23197	195	100.2	559	3659	84.2%
Cebidae	~19 My	22955	205	95.1	640	3466	84.9%
Colobinae	~14 My	23065	492	41.8	135	2486	89.2%
Strepsirrhini	~69 My	19914	161	113.8	420	1599	92.0%
Pan	~3 My	22819	133	160.3	869	1498	93.4%
Cercopithecidae	~19 My	25566	193	113.9	832	3588	86.0%
Ancestors in Rodents etc.	Age	Genes	Blocks	Average size (nb genes)	N50 size (nb genes)	Genes not in blocks	Coverage (%)
Glires	~81 My	22031	132	143.0	793	3156	85.7%
Myomorpha	~51 My	20924	161	114.9	490	2428	88.4%
Murinae	~20 My	20826	140	137.8	641	1534	92.6%
Hystricognathi	~42 My	20582	200	90.7	353	2449	88.1%
Mus	~7 My	20768	99	196.3	918	1338	93.6%
Rodentia	~80 My	21912	129	145.6	651	3130	85.7%
Mus_B	~2 My	21102	100	198.8	1033	1226	94.2%
Cricetidae	~20 My	20989	132	144.2	495	1960	90.7%
Cavia	~4 My	18062	323	53.3	202	830	95.4%
Lagomorpha	~48 My	18360	726	22.9	130	1751	90.5%
Cricetidae_B	~18 My	19411	250	72.7	248	1225	93.7%
Muroidea	~44 My	21858	116	166.0	841	2606	88.1%
Mus_A	~6 My	21067	106	186.2	927	1333	93.7%
Bathyergidae	~33 My	19565	278	63.4	189	1934	90.1%
Hystricomorpha_A	~32 My	18787	197	87.5	203	1548	91.8%
Hystricomorpha	~35 My	19717	179	99.1	311	1971	90.0%
Cricetulus griseus	(extant sp.)	20931	229	85.9	312	1265	94.0%
Sciurognathi	~79 My	21326	132	141.3	606	2679	87.4%
Cricetinae	~17 My	20439	146	129.3	550	1559	92.4%
Heterocephalus glaber	(extant sp.)	21465	596	32.3	102	2235	89.6%
Ancestors in Laurasiatherias	Age	Genes	Blocks	Average size (nb genes)	N50 size (nb genes)	Genes not in blocks	Coverage (%)
Insectivora	~68 My	15805	2624	2.7	3	8753	44.6%
Bovidae	~30 My	20299	161	116.5	505	1545	92.4%
Carnivora	~56 My	21040	105	178.7	768	2273	89.2%
Caniformia	~44 My	20267	139	133.2	569	1748	91.4%
Chiroptera	~60 My	18591	1131	15.0	35	1639	91.2%
Caniformia_b	~44 My	19624	397	45.9	123	1384	92.9%
Cetartiodactyla	~61 My	21430	161	118.6	618	2336	89.1%
Laurasiatheria	~88 My	23082	125	156.2	1007	3558	84.6%
Ancestors in mammals	Age	Genes	Blocks	Average size (nb genes)	N50 size (nb genes)	Genes not in blocks	Coverage (%)
Boreoeutheria	~95 My	24018	155	125.7	1023	4539	81.1%
Euarchontoglires	~90 My	23836	153	127.5	824	4336	81.8%
Diprotodontia	~65 My	18343	1787	8.3	14	3459	81.1%
Theria	~166 My	20786	350	49.1	261	3614	82.6%
Marsupialia	~148 My	19457	533	31.8	108	2531	87.0%
Eutheria	~102 My	22922	224	83.5	645	4207	81.6%
Mammalia	~184 My	20212	682	23.7	92	4066	79.9%
Xenarthra	~64 My	18956	2102	7.7	12	2850	85.0%
Atlantogenata	~100 My	20835	344	53.3	203	2498	88.0%
Afrotheria	~94 My	19431	395	44.3	138	1938	90.0%
Ancestors in fish	Age	Genes	Blocks	Average size (nb genes)	N50 size (nb genes)	Genes not in blocks	Coverage (%)
Poeciliinae	~100 My	21608	614	32.0	133	1967	90.9%
Atherinomorphae	~100 My	21684	459	42.4	501	2240	89.7%
Percomorphaceae	~125 My	22785	435	45.4	603	3043	86.6%
Tetraodontidae	~70 My	19047	615	27.5	311	2150	88.7%
Ovalentaria	~103 My	22257	380	51.9	572	2522	88.7%
Clupeocephala	~300 My	23093	2032	9.0	18	4747	79.4%
Acanthomorphata	~165 My	22526	1671	11.2	26	3871	82.8%
Eupercaria	~125 My	20915	432	43.6	305	2074	90.1%
Otophysi	~150 My	22612	1637	11.8	23	3245	85.6%
Ancestors in vertebrates	Age	Genes	Blocks	Average size (nb genes)	N50 size (nb genes)	Genes not in blocks	Coverage (%)
Euteleostomi	~420 My	19703	2268	6.0	9	6116	69.0%
Neopterygii	~330 My	19790	1459	10.5	22	4452	77.5%
Passeriformes	~45 My	15418	244	57.0	272	1510	90.2%
Vertebrata	~550 My	13436	536	2.3	2	12224	9.0%
Sarcopterygii	~400 My	19384	1529	9.8	19	4476	76.9%
Chordata	~550 My	10185	168	2.1	2	9826	3.5%
Ciona	~100 My	10842	1514	3.5	4	5597	48.4%
Galloanserae	~81 My	16328	281	52.2	324	1662	89.8%
Galliformes	~45 My	15606	217	66.0	327	1284	91.8%
Sauria	~267 My	18478	464	34.1	249	2656	85.6%
Neognathae	~105 My	16658	236	62.2	399	1984	88.1%
Amniota	~326 My	20133	452	35.5	271	4065	79.8%
Archelosauria	~250 My	17577	396	38.6	243	2273	87.1%
Tetrapoda	~359 My	19243	1021	14.8	36	4085	78.8%
Other ancestors	Age	Genes	Blocks	Average size (nb genes)	N50 size (nb genes)	Genes not in blocks	Coverage (%)
Bilateria	~580 My	8093	79	2.1	2	7928	2.0%
Fungi/Metazoa group	~1500 My	2232	37	2.1	2	2154	3.5%
Ecdysozoa	~580 My	7506	61	2.1	2	7378	1.7%

Genomicus — database version: 91.01 / Web-code version: 2017-06-13 — Dyogen Team