ID   JH374541; SV 1; linear; genomic DNA; CON; VRT; 1168 BP.
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AC   JH374541;
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PR   Project:PRJNA13342;
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DT   02-NOV-2011 (Rel. 110, Created)
DT   02-NOV-2011 (Rel. 110, Last updated, Version 1)
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DE   Gallus gallus chromosome 5 genomic scaffold, whole genome shotgun sequence.
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KW   .
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OS   Gallus gallus (chicken)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC   Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae;
OC   Phasianinae; Gallus.
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RN   [1]
RC   Erratum:[Nature. 2005 Feb 17;433(7027):777]
RP   1-1168
RX   DOI; 10.1038/nature03154.
RX   PUBMED; 15592404.
RG   International Chicken Genome Sequencing Consortium
RA   Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C., Ponting C.P.,
RA   Bork P., Burt D.W., Groenen M.A., Delany M.E., Dodgson J.B.,
RA   Chinwalla A.T., Cliften P.F., Clifton S.W., Delehaunty K.D., Fronick C.,
RA   Fulton R.S., Graves T.A., Kremitzki C., Layman D., Magrini V.,
RA   McPherson J.D., Miner T.L., Minx P., Nash W.E., Nhan M.N., Nelson J.O.,
RA   Oddy L.G., Pohl C.S., Randall-Maher J., Smith S.M., Wallis J.W., Yang S.P.,
RA   Romanov M.N., Rondelli C.M., Paton B., Smith J., Morrice D., Daniels L.,
RA   Tempest H.G., Robertson L., Masabanda J.S., Griffin D.K., Vignal A.,
RA   Fillon V., Jacobbson L., Kerje S., Andersson L., Crooijmans R.P., Aerts J.,
RA   van der Poel J.J., Ellegren H., Caldwell R.B., Hubbard S.J., Grafham D.V.,
RA   Kierzek A.M., McLaren S.R., Overton I.M., Arakawa H., Beattie K.J.,
RA   Bezzubov Y., Boardman P.E., Bonfield J.K., Croning M.D., Davies R.M.,
RA   Francis M.D., Humphray S.J., Scott C.E., Taylor R.G., Tickle C.,
RA   Brown W.R., Rogers J., Buerstedde J.M., Wilson S.A., Stubbs L.,
RA   Ovcharenko I., Gordon L., Lucas S., Miller M.M., Inoko H., Shiina T.,
RA   Kaufman J., Salomonsen J., Skjoedt K., Wong G.K., Wang J., Liu B., Wang J.,
RA   Yu J., Yang H., Nefedov M., Koriabine M., Dejong P.J., Goodstadt L.,
RA   Webber C., Dickens N.J., Letunic I., Suyama M., Torrents D., von Mering C.,
RA   Zdobnov E.M., Makova K., Nekrutenko A., Elnitski L., Eswara P., King D.C.,
RA   Yang S., Tyekucheva S., Radakrishnan A., Harris R.S., Chiaromonte F.,
RA   Taylor J., He J., Rijnkels M., Griffiths-Jones S., Ureta-Vidal A.,
RA   Hoffman M.M., Severin J., Searle S.M., Law A.S., Speed D., Waddington D.,
RA   Cheng Z., Tuzun E., Eichler E., Bao Z., Flicek P., Shteynberg D.D.,
RA   Brent M.R., Bye J.M., Huckle E.J., Chatterji S., Dewey C., Pachter L.,
RA   Kouranov A., Mourelatos Z., Hatzigeorgiou A.G., Paterson A.H., Ivarie R.,
RA   Brandstrom M., Axelsson E., Backstrom N., Berlin S., Webster M.T.,
RA   Pourquie O., Reymond A., Ucla C., Antonarakis S.E., Long M., Emerson J.J.,
RA   Betran E., Dupanloup I., Kaessmann H., Hinrichs A.S., Bejerano G.,
RA   Furey T.S., Harte R.A., Raney B., Siepel A., Kent W.J., Haussler D.,
RA   Eyras E., Castelo R., Abril J.F., Castellano S., Camara F., Parra G.,
RA   Guigo R., Bourque G., Tesler G., Pevzner P.A., Smit A., Fulton L.A.,
RA   Mardis E.R., Wilson R.K.;
RT   "Sequence and comparative analysis of the chicken genome provide unique
RT   perspectives on vertebrate evolution";
RL   Nature 432(7018):695-716(2004).
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RN   [2]
RP   1-1168
RG   International Chicken Genome Sequencing Consortium
RA   Hillier L.W., Warren W., Wilson R.K.;
RT   "Sequence assembly of the Gallus gallus genome version 4.0";
RL   Unpublished.
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RN   [3]
RP   1-1168
RG   International Chicken Genome Sequencing Consortium
RA   Hillier L.W., Warren W., Wilson R.K.;
RT   ;
RL   Submitted (19-SEP-2011) to the INSDC.
RL   Washington University School of Medicine, The Genome Institute, 4444 Forest
RL   Park, St. Louis, MO 63108, USA
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DR   MD5; e510cdcaff5169c8e7e2365fa45fe115.
DR   ENA; AADN030000000; SET.
DR   ENA; AADN000000000; SET.
DR   ENA-CON; CM000097.
DR   BioSample; SAMN02981218.
DR   Ensembl-Scaffolds; JH374541.1:1-1168; gallus_gallus.
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CC   The red jungle fowl (Gallus gallus) genome was originally sequenced
CC   to 6.6X coverage using a female known as 'RJF #256' from an inbred
CC   line (UCD 001), assembled (Gallus_gallus-1.0) and published in the
CC   December 9, 2004 issue of Nature. An additional
CC   198,000 directed sequence reads were completed and version
CC   Gallus_gallus-2.1 was released in 2006.  To address known gaps and
CC   17 Mb of erroneous duplications known to be in the Gallus_gallus
CC   2.1 version we have sequenced RJF #256 DNA to 12-fold genome
CC   coverage with the 454 platform and generated a new de novo
CC   assembly. This de novo assembly is derived from all previously
CC   generated Sanger reads and the newly generated 454 sequences using
CC   the CABOG assembler. The creation of the new chromosomal sequences
CC   proceeded in a way similar to that described for the original
CC   release (International Chicken Genome Sequencing Consortium, Nature
CC   2004) but benefited from the additional reads, improved assembly
CC   methods, and the improvements to the consensus genetic linkage
CC   maps. Further, the 85 finished RJF BAC clones were incorporated
CC   into the final chromosomal sequences, replacing underlying WGS
CC   contigs. This revised draft assembly (Gallus_gallus-4.0) was
CC   generated as part of our NHGRI-approved sequence assembly
CC   improvement plan for the existing draft assembly
CC   (Gallus_gallus-2.1) available on all major genome browsers. Ongoing
CC   sequence improvement efforts at The Genome Institute will continue
CC   on version Gallus_gallus-4.0. For questions regarding this
CC   Gallus_gallus-4.0 assembly please visit our existing chicken genome
CC   web page and contact the designated person for chicken. Funding for
CC   the sequence characterization of the chicken genome was provided by
CC   the National Human Genome Research Institute (NHGRI), National
CC   Institutes of Health (NIH).
CC   Of the 1.03 Gb genome Gallus_gallus-4.0, approximately 96% of the
CC   sequence has been anchored to chromosomes, which include autosomes
CC   1-28 and 32, two additional linkage groups, and sex chromosomes W
CC   and Z. A finished Z chromosome with 11 gaps was created from the
CC   manual assembly of sequenced BACs. All unknown gap sizes have been
CC   set to 100 bp. The N50 contig and supercontig lengths are 252kb
CC   (n=1185) and 17.6Mb (n=16).
CC   AGP Generation Details:
CC   In order to create chromosomal sequences, all four maps (consensus
CC   genetic map, East Lansing genetic map, physical map, and radiation
CC   hybrid map) were combined with the WGS assembly data. Using
CC   sequence comparison, marker sequences were assigned to contigs
CC   (contiguous stretches of DNA) in the WGS assembly. Based on these
CC   marker assignments, the supercontigs (sets of ordered/oriented
CC   contigs linked by virtue of read pairing data) were assigned to a
CC   chromosome based on a majority rule (>50% of markers assigned to
CC   the same chromosome). The supercontigs were initially positioned
CC   along chromosomes based on their median marker position, and
CC   initially oriented based on relative marker order along the
CC   supercontig.  The physical map was also linked to the sequence
CC   assembly by using BAC end sequence links and in silico digests of
CC   the assembly to create 'ultracontigs' ordered/oriented lists of
CC   'supercontigs'. Following these initial placements, the WGS
CC   assembly read pairing data were used, where possible, to aid in
CC   orientation and confirm order.  All discrepancies between the
CC   various maps were manually reviewed and a combined
CC   super/ultracontig order was established based on reconciling the
CC   data from all four maps. Alignments against all available Gallus
CC   gallus mRNAs were used as well in defining order and orientation
CC   where possible.  Sequences from finished Gallus gallus RJF clones
CC   were also incorporated into the final AGP files. Alignments with
CC   the human genome were also examined and used as aid in orientation
CC   particularly when available chicken marker data were
CC   inconclusive.The final step was to incorporate finished BAC clones
CC   into the assembly.  Out of 193 finished BAC clones 108 mapped
CC   completely into contiguous sequence with >99.99% identity. The
CC   remaining 85 were incorporated into the assembled autosomes,
CC   replacing the underlying WGS contigs.
CC   ##Genome-Assembly-Data-START##
CC   Assembly Name         :: Gallus_gallus-4.0
CC   Sequencing Technology :: Sanger; 454
CC   ##Genome-Assembly-Data-END##
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FH   Key             Location/Qualifiers
FH
FT   source          1..1168
FT                   /organism="Gallus gallus"
FT                   /chromosome="5"
FT                   /isolate="#256"
FT                   /mol_type="genomic DNA"
FT                   /sex="female"
FT                   /note="breed: Red Jungle fowl, inbred line UCD001"
FT                   /db_xref="taxon:9031"
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CO   join(complement(AADN03004887.1:1..1168))
//