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 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

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