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채한화 (Han-Ha Chai) 저자 이메일 보기
전남대학교, 국립축산과학원
조회 17  인쇄하기 주소복사 트위터 공유 페이스북 공유 
Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye
열기 Authors and Affiliations

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.
논문정보
- 형식: Research article
- 게재일: 2018년 07월 (BRIC 등록일 2018-07-30)
- 연구진: 국내연구진태극기
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관련인물
김준모 (중앙대학교)
남경우 (한양대학교)
남진우 (한양대학교)
손장일 (한양대학교)
홍효선 (한양대학교)
외부링크
Google (by Han-Ha Chai)
Pubmed (by Han-Ha Chai)
프리미엄 Bio일정 Bio일정 프리미엄 안내
제2회 오가노이드 심포지엄 및 핸즈온워크샵 [2019 CHA Organoid Center Symposium]
제2회 오가노이드 심포지엄 및 핸즈온워크샵 [2019 CHA Organoid Center Symposium]
날짜: 2019.05.09
장소: 판교 차바이오컴플렉스 국제회의실
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