Abstract
Yeonsan Ogye (YO), an indigenous Korean chicken breed (gallus gallus domesticus), has entirely black external features and internal organs. In this study, the draft genome of YO was assembled using a hybrid de novo assembly method that takes advantage of high-depth Illumina short-reads (232.2X) and low-depth PacBio long-reads (11.5X). Although the contig and scaffold N50s (defined as the shortest contig or scaffold length at 50% of the entire assembly) of the initial de novo assembly were 53.6Kbp and 10.7Mbp, respectively, additional and pseudo-reference-assisted assemblies extended the assembly to 504.8Kbp for contig N50 (pseudo-contig) and 21.2Mbp for scaffold N50, which included 211,827 retrotransposons and 27,613 DNA transposons. The completeness (97.6%) of the YO genome was evaluated with BUSCO, and found to be comparable to the current chicken reference genome (galGal5; 97.4%), which was assembled with a long read-only method, and superior to other avian genomes (92~93%), assembled with short read-only and hybrid methods. To comprehensively reconstruct transcriptome maps, RNA sequencing (RNA-seq) data were analyzed from twenty different tissues, including black tissues. The maps included 15,766 protein-coding and 6,900 long non-coding RNA genes. By comparing to the gallus gallus red junglefowl chicken reference genome and re-sequencing data from additional YO chickens, 551 large structural variants, 895,988 single nucleotide polymorphisms, and 82,392 small insertions/deletions were detected across the YO genome.