de novo Assembly of the Chinese Bamboo-Partridge Genome and Comparison with Chicken

History of chicken domestication at the genome level is not completely resolved, in particular the possible contribution of Gallus species different from Red junglefowl Gallus gallus. In the context of a larger project (Domestichick), which addresses the question of chicken domestication using molecular approaches, we undertook the sequencing and de novo assembly of the Chinese bamboo-partridge genome (Bambusicola thoracica), sister taxon of the four Gallus species. We used three different libraries (paired-end, 3 kb and 6 kb mate-pairs), sequenced each at 50X coverage. Taking advantage of the close phylogenetic relationship between Bambusicola and the chicken, confirmed by the ability to align more than 95% of the reads against the chicken genome with ~95% identity, the reads were first partitioned according to chicken chromosomes based on sequence similarities and then de novo assembled using the masurca software within each chromosome. The resulting assembly totalizes 920 Mb of sequences assembled into scaffolds with a N50 scaffold length of 2.5 Mb. The resulting scaffolds were aligned to the chicken chromosomes. The extent of conservation between the newly assembled Bambusicola genome and the chicken genome will be presented.