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

Title
Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye
Author
남진우
Keywords
Gallus gallus domesticus; Yeonsan Ogye; whole genome de novo assembly; transcriptome maps; hyperpigmentation
Issue Date
2018-07
Publisher
OXFORD UNIV PRESS
Citation
GIGASCIENCE, v. 7, no. 7
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.
URI
https://academic.oup.com/gigascience/article/7/7/giy086/5052204https://repository.hanyang.ac.kr/handle/20.500.11754/119384
ISSN
2047-217X
DOI
10.1093/gigascience/giy086
Appears in Collections:
COLLEGE OF NATURAL SCIENCES[S](자연과학대학) > LIFE SCIENCE(생명과학과) > Articles
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