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The chicken genome that was sequenced is from the inbred line UCD001, which was derived from a wild population of red jungle fowl in Malaysia in the late 1930s. There is the possible introgression of a limited amount of ... White Leghorn genome during the captive breeding history. All sequencing libraries were prepared from DNA of a single female of the inbred line to minimize heterozygosity and provide sequence for both sex chromosomes. (The female chicken is heterogametic (ZW) and the male is homogametic (ZZ).). The 01 version of the project was generated using PCAP from approximately 6.6X coverage in whole-genome shotgun reads and a combination of plasmid, fosmid and bacterial artificial chromosome (BAC)-end read pairs. From that assembly, 198,000 additional reads were ordered to cover all contig ends and regions of low quality. This 02 version is the result of a new PCAP assembly that was generated from the sequence improvement reads as well as the original 6.6X coverage. In addition, the original release markers have been added to the various maps (consensus linkage map, East Lansing map, radiation hybrid map, physical map). The creation of the new chromosomal sequences proceeded in a way similar to that described for the original release (International Chicken Genome Sequencing Consortium, 2004) but benefited from the additional reads, improved assembly methods, and the addition of the RH and East Lansing maps and the significantly improved genetic and physical maps. Further, 100 finished RJF clones were incorporated into the final chromosomal sequences, replacing underlying WGS contigs.
Of the 1.05 Gb genome, approximately 95% of the sequence has been anchored to chromosomes, which include autosomes 1-28 and 32, plus 3 additional linkage groups, and sex chromosomes W and Z.  more

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