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Gallus_gallus-5.0

Organism name:
Gallus gallus (chicken)
Infraspecific name:
Breed: Red Jungle fowl, inbred line UCD001
Isolate:
RJF #256
Sex:
female
BioSample:
SAMN02981218
BioProject:
PRJNA13342
Submitter:
International Chicken Genome Consortium
Date:
2015/12/16
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_000002315.3 (replaced)
RefSeq assembly accession:
GCF_000002315.4 (replaced)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT (in non-nuclear assembly-unit)
  • Data displayed for RefSeq version
WGS Project:
AADN04
Assembly method:
MHAP/PBcR v. 8.2beta
Genome coverage:
70x
Sequencing technology:
Sanger; 454; Illumina; PacBio

IDs: 595851 [UID] 2725238 [GenBank] 2727418 [RefSeq]

See Genome Information for Gallus gallus

There are 2 assemblies for this organism

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History (Show revision history)

Comment


 The previous red jungle fowl (Gallus gallus) genome assembly, version Gallus_gallus-4.0, was sequenced and assembled with varied sequencing technology, including Sanger, Illumina and 454. In recognition of the need for sequence assembly improvement we have sequenced the same ... DNA reference source, a female known as "RJF #256" from an inbred line (UCD 001), on the Pacific Biosciences RSII instrument (a relatively equal split of P4 and P5 chemistry reads) to roughly 70x genome coverage and assembled all reads with the MHAP/PbCR algorithm. The creation of the new chromosomal sequences proceeded in a way similar to that described for the original release (International Chicken Genome Sequencing Consortium, Nature 2004) but benefited from the longer read lengths, improved assembly methods, and the availablity of additional physical maps (see Credits). In an attempt to avoid loss of sequence in the transition from Gallus_gallus-4.0 to Gallus_gallus-5.0 we merged each into one assembly using graph accordance methods (Yao et. al. 2011. Bioinformatics). Furthermore, where appropriate, finished RJF BAC clones were incorporated into the final chromosomal sequences, replacing underlying WGS contigs. This new draft assembly (Gallus_gallus-5.0) was generated as part of our USDA-approved sequence assembly improvement plan for the existing draft assembly (Gallus_gallus-4.0) available on all major genome browsers. Ongoing sequence improvement efforts at the McDonnell Genome Institute will continue on version Gallus_gallus-5.0 for future updates. For questions regarding this Gallus_gallus-5.0 assembly please visit our existing chicken genome web page and contact the designated person for chicken. Funding for the sequence characterization of the chicken genome was provided by the USDA, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH) and Cobb Vantress.
 The 1.21 Gb genome Gallus_gallus-5.0 includes sequences assigned to the autosomes 1-28 and 30-33, one additional linkage group, and sex chromosomes W (a combination of finished BACs and de novo contigs) and Z. A finished Z chromosome with only a few remaining gaps was created from the manual assembly of sequenced BACs (see Credits).The remaining unanchored contigs have been assembled into unplaced scaffolds named "chrUn_Scaffold*". All unknown gap sizes have been set to 100 bp. The total assembly N50 contig and scaffold lengths are 2.6Mb (n=116) and 6.4Mb (n=47). 
 Although centromere positions are indicated in Gallus_gallus-5.0, little is known of their exact sequence. The centromeres of 18 chromosomes were tentatively localized based on prior information used to localize these structures in previous versions, including FISH hybridization using BAC clones, genetic markers flanking the centromeres in coordination with mapping gaps in the physical map, repetitive sequence content, and analysis of proximity to the constrictions of the mitotic metaphase chromosomes. Macrochromosome centromere sizes were assigned arbitrarily to be 1.5 Mb and those of microchromosomes to be 0.5 Mb lengths in absence of any evidence as to their true lengths.
 AGP Generation Details:
 In order to create chromosomal sequences, all four maps (consensus genetic map, East Lansing genetic map, physical map, and radiation hybrid map) were combined with the WGS assembly data. Using sequence comparison, marker sequences were assigned to contigs (contiguous stretches of DNA) in the WGS assembly. Based on these marker assignments, the supercontigs (sets of ordered/oriented contigs linked by virtue of read pairing data) were assigned to a chromosome based on a majority rule (>50% of markers assigned to the same chromosome). The supercontigs were initially positioned along chromosomes based on their median marker position, and initially oriented based on relative marker order along the supercontig. The physical map was also linked to the sequence assembly by using BAC end sequence links and in silico digests of the assembly to create "ultracontigs" ordered/oriented lists of "supercontigs". Following these initial placements, the WGS assembly read pairing data were used, where possible, to aid in orientation and confirm order. All discrepancies between the various maps were manually reviewed and a combined super/ultracontig order was established based on reconciling the data from all four maps. Alignments against all available Gallus gallus mRNAs were used as well in defining order and orientation where possible. Sequences from finished Gallus gallus RJF clones were also incorporated into the final AGP files. Alignments with the human genome were also examined and used as aid in orientation particularly when available chicken marker data were inconclusive.
 Credits:
 Sequencing - McDonnell Genome Institute at Washington University School of Medicine, St. Louis. Assembly, Assembly/Map Integration, Golden Path Creation - LaDeana Hillier, Chad Tomlinson, Pat Minx, Wesley Wa  more

Global statistics

Total sequence length1,230,258,557
Total ungapped length1,218,493,558
Gaps between scaffolds397
Number of scaffolds23,870
Scaffold N506,379,610
Scaffold L5047
Number of contigs24,693
Contig N502,894,815
Contig L50110
Total number of chromosomes and plasmids36
Number of component sequences (WGS or clone)25,475

Supplemental Content

PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
non-nuclear
Assembly Unit: Primary Assembly (GCF_000000185.3)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM000093.4=NC_006088.41,779
Chromosome 2CM000094.4=NC_006089.41,147
Chromosome 3CM000095.4=NC_006090.4780
Chromosome 4CM000096.4=NC_006091.4617
Chromosome 5CM000097.4=NC_006092.4416
Chromosome 6CM000098.4=NC_006093.4245
Chromosome 7CM000099.4=NC_006094.4249
Chromosome 8CM000100.4=NC_006095.4249
Chromosome 9CM000101.4=NC_006096.4158
Chromosome 10CM000102.4=NC_006097.4147
Chromosome 11CM000103.4=NC_006098.4167
Chromosome 12CM000104.4=NC_006099.4138
Chromosome 13CM000105.4=NC_006100.4163
Chromosome 14CM000106.4=NC_006101.4117
Chromosome 15CM000107.4=NC_006102.482
Chromosome 16CM000108.4=NC_006103.421
Chromosome 17CM000109.4=NC_006104.484
Chromosome 18CM000110.4=NC_006105.464
Chromosome 19CM000111.4=NC_006106.478
Chromosome 20CM000112.4=NC_006107.4156
Chromosome 21CM000113.4=NC_006108.451
Chromosome 22CM000114.4=NC_006109.480
Chromosome 23CM000115.4=NC_006110.466
Chromosome 24CM000116.4=NC_006111.445
Chromosome 25CM000124.4=NC_006112.391
Chromosome 26CM000117.4=NC_006113.429
Chromosome 27CM000118.4=NC_006114.464
Chromosome 28CM000119.4=NC_006115.445
Chromosome 30CM003637.1=NC_028739.19
Chromosome 31CM003638.1=NC_028740.111
Chromosome 32CM000120.3=NC_006119.39
Chromosome 33CM000123.4=NC_008465.317
Chromosome WCM000121.4=NC_006126.4108
Chromosome ZCM000122.4=NC_006127.4528
Linkage Group LGE64CM000367.3=NC_008466.318
unplacedn/an/an/a15,411

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule1,230,241,78223,8691,218,476,7836,379,610823397
Chromosome 1AllAssembled moleculeUnlocalized scaffolds210,673,733196,202,54414,471,1891,859801,779209,547,246195,118,62114,428,6259,917,5739,917,57310,647108773179790
Chromosome 2AllAssembled moleculeUnlocalized scaffolds158,710,615149,560,7359,149,8801,210631,147157,657,877148,532,3679,125,5106,722,9639,100,70910,05086582862620
Chromosome 3AllAssembled moleculeUnlocalized scaffolds116,920,747111,302,1225,618,62580020780116,229,657110,624,8575,604,8008,843,6268,843,6268,70840281219190
Chromosome 4AllAssembled moleculeUnlocalized scaffolds96,543,41891,282,6565,260,7626382161795,854,70590,606,7045,248,00118,075,63418,075,63410,33237211620200
Chromosome 5AllAssembled moleculeUnlocalized scaffolds63,034,72859,825,3023,209,4264382241662,493,50559,289,4163,204,0898,193,01229,922,9619,8061913621210
Chromosome 6AllAssembled moleculeUnlocalized scaffolds37,500,17335,467,0162,033,1572591424536,970,68234,941,9482,028,7345,065,9165,065,91610,8091712514140
Chromosome 7AllAssembled moleculeUnlocalized scaffolds38,707,05336,946,9361,760,117255624938,081,18636,327,2711,753,9159,789,0169,789,0169,0831486550
Chromosome 8AllAssembled moleculeUnlocalized scaffolds32,086,49129,963,0132,123,478256724931,481,19929,362,7512,118,4488,083,0498,083,04911,3711064660
Chromosome 9AllAssembled moleculeUnlocalized scaffolds25,237,18724,091,5661,145,621163515824,692,06223,549,8461,142,2166,715,4996,715,4998,7521174550
Chromosome 10AllAssembled moleculeUnlocalized scaffolds21,385,62520,435,342950,283156914720,870,62219,928,132942,4905,957,9975,957,9978,4571376990
Chromosome 11AllAssembled moleculeUnlocalized scaffolds21,449,82220,218,7931,231,0291821516720,941,62319,711,9771,229,6462,511,8652,511,86510,090119214140
Chromosome 12AllAssembled moleculeUnlocalized scaffolds21,002,08919,948,1541,053,935142413820,996,11219,946,1771,049,93516,769,34816,769,3489,410633000
Chromosome 13AllAssembled moleculeUnlocalized scaffolds19,897,46618,407,4601,490,0061832016319,385,11117,898,9921,486,1194,626,8754,626,87512,648107320200
Chromosome 14AllAssembled moleculeUnlocalized scaffolds16,681,24415,595,0521,086,192125811716,175,97915,093,6281,082,35112,743,02012,743,02015,377523770
Chromosome 15AllAssembled moleculeUnlocalized scaffolds13,353,50612,762,846590,6608428213,351,51812,762,215589,30310,533,77810,533,7789,054413110
Chromosome 16AllAssembled moleculeUnlocalized scaffolds1,058,524652,338406,186298211,053,434649,799403,635125,648145,39132,664752770
Chromosome 17AllAssembled moleculeUnlocalized scaffolds11,686,89110,956,400730,4919068411,182,45910,451,968730,49110,324,02710,324,02711,828550660
Chromosome 18AllAssembled moleculeUnlocalized scaffolds11,426,50211,053,727372,7756736411,422,62211,050,210372,4124,149,4944,149,4948,157431220
Chromosome 19AllAssembled moleculeUnlocalized scaffolds10,716,9169,979,828737,0887917810,714,8489,978,356736,4929,979,8289,979,82813,096431000
Chromosome 20AllAssembled moleculeUnlocalized scaffolds15,720,94914,109,3711,611,578161515615,627,85514,019,6931,608,16212,604,75212,604,75214,929954440
Chromosome 21AllAssembled moleculeUnlocalized scaffolds7,159,5176,862,722296,795543517,153,4816,858,574294,9076,515,0676,515,0677,079642220
Chromosome 22AllAssembled moleculeUnlocalized scaffolds5,435,3684,729,743705,625877804,926,4824,221,847704,6351,342,7921,342,79211,8111082660
Chromosome 23AllAssembled moleculeUnlocalized scaffolds6,289,3135,786,528502,785693666,280,3625,777,577502,7853,733,7563,733,75616,90713130220
Chromosome 24AllAssembled moleculeUnlocalized scaffolds6,631,7026,280,547351,155461456,627,9546,278,001349,9536,280,5476,280,5479,309431000
Chromosome 25AllAssembled moleculeUnlocalized scaffolds3,644,5902,906,300738,29011221913,129,2312,391,866737,365236,253324,51711,7321210220200
Chromosome 26AllAssembled moleculeUnlocalized scaffolds5,546,5725,313,770232,802323295,533,0865,301,280231,8064,044,2404,044,24010,351862220
Chromosome 27AllAssembled moleculeUnlocalized scaffolds6,304,8385,655,794649,0448319646,190,1865,543,052647,134793,546825,30818,213108218180
Chromosome 28AllAssembled moleculeUnlocalized scaffolds5,243,7144,974,273269,441516455,231,4374,961,996269,4411,385,9061,385,9067,21810100550
Chromosome 30AllAssembled moleculeUnlocalized scaffolds224,32124,927199,3941019222,34423,787198,55724,92724,92729,556211000
Chromosome 31AllAssembled moleculeUnlocalized scaffolds168,86449,161119,70314311168,66448,961119,70316,53525,95714,106000220
Chromosome 32AllAssembled moleculeUnlocalized scaffolds253,55278,254175,2981239251,64878,054173,59444,77559,03944,775303220
Chromosome 33AllAssembled moleculeUnlocalized scaffolds3,756,4411,648,0312,108,410247173,747,7901,645,1362,102,654388,401388,4011,265,006725660
Chromosome WAllAssembled moleculeUnlocalized scaffolds7,082,4555,160,0351,922,420125171086,505,5124,596,9991,908,513285,806362,16832,5612952416160
Chromosome ZAllAssembled moleculeUnlocalized scaffolds88,942,39382,310,1666,632,2275381052888,363,70481,904,1716,459,53311,056,05911,056,05920,29144539990
Linkage Group LGE64AllAssembled moleculeUnlocalized scaffolds1,217,975897,576320,399257181,214,728894,329320,399208,615208,61521,252330660
unplacedAssembled molecule138,546,48815,411138,199,87212,5462420
MoleculeTotal
Length
Mitochondrion MT16,775
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