A Improved Chicken Genome Reference: Recovery of Missing Autosomes and Addition of a New W Chromosome

Given the continued intense interest in and need for improvement of the chicken genome reference (Gallus_gallus-5.0) we have built a new preliminary version of the chicken genome (temporarily termed Gallus_gallus-6.0) using single molecule real-time technology (SMRT). The assembled contigs were ordered and oriented (i.e. scaffolded) using a new proximity-based chromatin map to allocate sequences to all autosomes. We sequenced the same Red Jungle fowl reference DNA to ~80x coverage and generated the chromatin proximity map from this same source. Total assembled bases were 1.05Gb, with an N50 contig and scaffold lengths of 16Mb and 90Mb, respectively. Of the 1.05 Gb genome, 94% of the sequence anchored to 39 scaffolds (chromosomes). In addition to sequences for previously ‘missing’ chromosomes we also have significantly improved the representation of the W chromosome using targeted BAC selection, sequencing, and local assembly. The W chromosome assembled to ~7Mb revealed islands of euchromatin sequence containing 28 genes with no acquired genes and interestingly with none showing exclusive expression in the ovary. Currently we are working to develop chromosome formatted files, resolve assembly error, integrate finished BACs and number the previously missing autosomes to provide the community a more complete and accurate reference.