Supporting data for "Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye"

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 (376.6X) and low-depth PacBio long-reads (9.7X). The contig and scaffold NG50s of the hybrid de novo assembly were 362.3Kbp and 16.8Mbp, respectively. The completeness (97.6%) of the draft genome (Ogye_1.1) was evaluated with single copy orthologous genes using BUSCO, and found to be comparable to the current chicken reference genome (galGal5; 97.4%; contigs were assembled with high-depth PacBio long-reads (50X) and scaffolded with short-reads), and superior to other avian genomes (92~93%; assembled with short-read-only or hybrid methods). Compared to galGal4 and 5, the draft genome included 551 structural variations including the Fibromelanosis (FM) locus duplication, related to hyperpigmentation. To comprehensively reconstruct transcriptome maps, RNA sequencing (RNA-seq) and reduced representation bisulfite sequencing (RRBS) data were analyzed from twenty different tissues, including four black tissues (skin, shank, comb, and fascia). The maps included 15,766 protein-coding and 6,900 long non-coding RNA genes, many of which were tissue-specifically expressed and displayed tissue-specific DNA methylation patterns in the promoter regions. We expect that the resulting genome sequence and transcriptome maps will be valuable resources for studying domestic chicken breeds, including black-skinned chickens, as well as for understanding genomic differences between breeds and the evolution of hyperpigmented chickens and functional elements related to hyperpigmentation.