On Nov 21, 2011 this sequence version replaced gi:354542463.
The Gallus gallus whole genome shotgun (WGS) project has the project accession AADN00000000. This version of the project (03) has the accession number AADN03000000, and consists of sequences AADN03000001-AADN03027102.
The red jungle fowl (Gallus gallus) genome was originally sequenced to 6.6X coverage using a female known as 'RJF #256' from an inbred line (UCD 001), assembled (Gallus_gallus-1.0) and published in the December 9, 2004 issue of Nature. In recognition of the need for sequence assembly improvement an additional
198,000 directed sequence reads were completed and version Gallus_gallus-2.1 was released in 2006. To address known gaps and
17 Mb of erroneous duplications known to be in the Gallus_gallus 2.1 version we have sequenced RJF #256 DNA to 12-fold genome coverage with the 454 platform and generated a new de novo assembly. This de novo assembly is derived from all previously generated Sanger reads and the newly generated 454 sequences using the CABOG assembler (see Credits). 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 additional reads, improved assembly methods, and the improvements to the consensus genetic linkage maps (see Credits). Further, the 85 finished RJF BAC clones were incorporated into the final chromosomal sequences, replacing underlying WGS contigs. This revised draft assembly (Gallus_gallus-4.0) was generated as part of our NHGRI approved sequence assembly improvement plan for the existing draft assembly (Gallus_gallus-2.1) available on all major genome browsers. Ongoing sequence improvement efforts at The Genome Institute will continue on version Gallus_gallus-4.0. For questions regarding this Gallus_gallus-4.0 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 National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).
Of the 1.03 Gb genome Gallus_gallus-4.0, approximately 96% of the sequence has been anchored to chromosomes, which include autosomes 1-28 and 32, two additional linkage groups, and sex chromosomes W and Z. (In contrast to mammals, the female chicken is heterogametic (ZW) and the male is homogametic (ZZ).) A finished Z chromosome with 11 gaps was created from the manual assembly of sequenced BACs (see Credits). All unknown gap sizes have been set to 100 bp. The N50 contig and supercontig lengths are 252kb (n=1185) and 17.6Mb (n=16).
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.The final step was to incorporate finished BAC clones into the assembly. Out of 193 finished BAC clones 108 mapped completely into contiguous sequence with >99.99% identity. The remaining 85 were incorporated into the assembled autosomes, replacing the underlying WGS contigs.
Sequencing - The Genome Institute at Washington University School of Medicine, St. Louis.
Physical Map - The Genome Institute at Washington University School of Medicine, St. Louis.
Assembly, Assembly/Map Integration, Golden Path Creation - Aleksey V. Zimin, Michael Roberts and James A. Yorke, Institute for Physical Science and Technology, University of Maryland, College Park; LaDeana Hillier, Pat Minx, Wesley Warren, The Genome Institute at Washington University School of Medicine, St. Louis.
Assembly submission - Shunfang Hou, The Genome Institute at Washington University School of Medicine, St. Louis.
Genetic Mapping/Linkage Analysis - The Chicken Mapping Consortium:
Wageningen Map based on Wageningen broilerxbroiler mapping population ('W' linkage maps; 460 F2 animals), coordinated by Martien Groenen, Wageningen University.
East Lansing Map based on the RJFxlayer cross ('E' linkage maps; 56 BC animals), coordinated by Hans Cheng, USDA, ARS, East Lansing, MI.
Compton map based on layerxlayer cross ('C' linkage maps; 52 BC animals), coordinated by Nat Bumstead, Institute for Animal Health.
Consensus linkage map: Martien Groenen and Richard Crooijmans, Wageningen University.
RH map: coordinated by Mireille Morisson and Alain Vignal, INRA Toulouse, http://chickrh.toulouse.inra.fr
Linkage Mapping: White Leghorn X Red Junglefowl (800 F2 animals), Susanne Kerje, Lina Jacobsson and Leif Andersson, Uppsala University
Clone/Marker Pairs: coordinated by Jerry Dodgson, Michigan State University.
Marker Name/Sequence Resolution: coordinated by Hans Cheng, USDA, ARS, East Lansing, MI.
Chicken FPC browser: http://www.animalsciences.nl/ChickFPC/, Martien Groenen and Richard Crooijmans, Wageningen University.
Additional Mapping Data Contributions : Winston Bellott (David Page Lab, WIBR-MIT)
cDNA sequences - http://ncbi.nlm.nih.gov and http://chick.umist.ac.uk
RJF finished clones - NIH Intramural Sequencing Center (NISC) at the NIH (AC091708.2, AC094012.2, AC138565.3; S. Kerje and L. Andersson at Uppsala University (AY636124.1). The Genome Institute at Washington University School of Medicine, St. Louis, MO (all others).
Finished Z chromosome: Winston Bellot, WIBR-MIT, Cambridge, MA; The Genome Institute at Washington University School of Medicine, St. Louis, MO. Reference cited for Z chromosome use: Bellot et al. 2010. Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. 466:61. Nature.
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