Chicken Genome PROPOSAL TO ENHANCE THE SEQUENCE OF THE CHICKEN GENOME

The chicken genome (~1.2 Gb) was sequenced with NIH support in response to a White Paper (see http://genome.wustl.edu/genomes/view/gallus_gallus/ ) by the Washington U. Genome Sequencing Center (WUGSC) with the first draft sequence announced in March 2004. That draft was based on 6.6X WGS (Sanger) coverage, assembled and aligned to chromosomes using BAC end sequences and a comprehensive BAC physical map (Wallis et al., 2004). DNA from a single, partially inbred Red Jungle Fowl bird (the primary wild progenitor of domestic chickens) was sequenced. Subsequently, a second Build (WUGSC 2.1/galGal3) was generated, and this build is currently available on the genome browsers. It added an additional 198K reads focused on contig ends and regions of poor quality. Furthermore, the assembly was improved using early SNP mapping data that better aligned contigs on chromosomes. Total sequence in Build 2 includes 1.1 Gb of sequence, about 95% of which is anchored to autosomes 1-28 and 32, along with the Z and W sex chromosomes. A small amount of sequence is assigned to linkage groups for which numbered chromosomes are not available (chicken has 39 chromosome pairs) and 63.9 Mb of sequence remained on chrUn_random. A relatively small part of the sequence is on chromosome-specific unassembled contigs. The Z and W sex chromosomes were sequenced only to ~3.3X due to their hemizygous state in the female bird used. Build 2.1 increased the size of chrZ from 33.6 to 74.6 Mb and decreased chrW from 4.9 Mb to 0.26 Mb due, in part, to several mistaken assignments of contigs to W in Build 1 that were actually on Z. For Build 2, the contig N50 = 45 kb, the supercontig N50 = 11.1 Mb and the ultracontig N50 = 15.5 Mb. The difference between the first two statistics reflects a fairly high frequency of short unsequenced gaps spanned by read pairs. Nevertheless, by a variety of measures, the Build 2 assembly is of very high quality. This is probably due, in part, to the much lower level of interspersed repeats in avian genomes (~10%) vs. mammalian genomes (>30%).