Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye

  1. Jang-il Sohn
  2. Kyoungwoo Nam
  3. Hyosun Hong
  4. Jun-Mo Kim
  5. Dajeong Lim
  6. Kyung-Tai Lee
  7. Yoon Jung Do
  8. Chang Yeon Cho
  9. Namshin Kim
  10. Han-Ha Chai
  11. Jin-Wu Nam

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Abstract

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.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giy086

    Jang-il Sohn 1Department of Life Science, Hanyang University, Seoul 133-791, Republic of Korea2Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 133-791, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKyoungwoo Nam 1Department of Life Science, Hanyang University, Seoul 133-791, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHyosun Hong 1Department of Life Science, Hanyang University, Seoul 133-791, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJun-Mo Kim 3Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju 55365, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDajeong Lim 3Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju 55365, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteKyung-Tai Lee 3Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju 55365, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteYoon Jung Do 3Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju 55365, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChang Yeon Cho 4Animal Genetic Resource Research Center, National Institute of Animal Science, RDA, Namwon 55717, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNamshin Kim 5Personalized Genomic Medicine Research Center, KRIBB, Daejeon 34141, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteHan-Ha Chae 3Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju 55365, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJin-Wu Nam 1Department of Life Science, Hanyang University, Seoul 133-791, Republic of Korea2Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 133-791, Republic of KoreaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy086 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101252 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101253

  2. Version published to 10.1093/gigascience/giy086
  3. Version published to 10.1101/224311v3 on bioRxiv
  4. Version published to 10.1101/224311v2 on bioRxiv
  5. Version published to 10.1101/224311v1 on bioRxiv