Authors and Affiliations

Authors and Affiliations

Jang-il Sohn^1,2,†, Kyoungwoo Nam^1,†, Hyosun Hong^1,†, Jun-Mo Kim^3,†, Dajeong Lim⁴, Kyung-Tai Lee⁴, Yoon Jung Do⁴, Chang Yeon Cho⁵, Namshin Kim⁶, Han-Ha Chai^4,7,* and Jin-Wu Nam <sup>1,2,*

1</sup>Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea, ²Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 133-791, Republic of Korea, ³Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea, ⁴Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea, ⁵Animal Genetic Resource Research Center, National Institute of Animal Science, RDA, Namwon, 55717, Republic of Korea, ⁶Personalized Genomic Medicine Research Center, KRIBB, Daejeon, 34141, Republic of Korea and ⁷College of Pharmacy, Chonnam National University, Kwangju, 61186, Republic of Korea 

^*Correspondence address.Jin-Wu Nam, Han-Ha Chai

^†These authors contributed equally

Background

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 Pacific Biosciences (PacBio) long reads (9.7X).

Findings

The contig and scaffold NG50s of the hybrid de novo assembly were 362.3 Kbp and 16.8 Mbp, respectively. The completeness (97.6%) of the draft genome (Ogye_1.1) was evaluated with single-copy orthologous genes using Benchmarking Universal Single-Copy Orthologs 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 galGal5, the draft genome included 551 structural variations including the fibromelanosis (FM) locus duplication, related to hyperpigmentation. To comprehensively reconstruct transcriptome maps, RNA sequencing and reduced representation bisulfite sequencing data were analyzed from 20 tissues, including 4 black tissues (skin, shank, comb, and fascia). The maps included 15,766 protein-coding and 6,900 long noncoding RNA genes, many of which were tissue-specifically expressed and displayed tissue-specific DNA methylation patterns in the promoter regions.

Conclusions

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.