De novo Sequencing and Analysis of a Korean Native Black Chicken Genome, Heuksaek Jaerae-jong

The Heuksaek Jaerae-jong-gae is one of the indigenous chicken breeds registered with Food and Agricultural Organization. This native chicken breed has been raised across the Korean peninsula and it is widely known to have a robustness against diseases. Although there is a Chicken reference assembly available, it is still important to sequence a local breed to elucidate its genomic feature. Here we report the current progress of the de novo genome sequencing of a female Heuksaek Jaerae-jong-gae using Illumina HiSeq 2000 platform. Multiple insert-size libraries were constructed including two types of 97 bp paired-end libraries (170 bp and 500 bp) and three types of 87 bp mate-pair libraries (2 Kbp, 5 Kbp and 10 Kbp). It resulted in a total of approximately 180 Gbp (120 Gbp from paired-end, 60 Gbp from mate-pair) corresponding to 171-fold coverage. De novo assembly was performed using AllPaths-LG with default setting. Gaps in the assembled scaffolds were filled using GapCloser. As a result, we obtained the Heuksaek Jaerae-jong-gae draft genome of 1.02 Gbp. The genome size of the native breed was similar with the current chicken reference assembly (galGal 4). The Scaffold N50 and contig N50 size were 8.6 Mbp and 99 Kbp respectively, showing a reasonable quality of the Heuksaek Jaerae-jong-gae assembly. We also predicted 22,900 genes, and 550,922 repeat elements were identified masking 10.1% of the genome. Further investigation to dissect the genome is currently undergoing. We expect that our study be a useful resource for comparative genome analysis between diverse chicken breeds.