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dc.contributor.author남진우-
dc.date.accessioned2019-12-08T14:32:12Z-
dc.date.available2019-12-08T14:32:12Z-
dc.date.issued2018-07-
dc.identifier.citationGIGASCIENCE, v. 7, no. 7en_US
dc.identifier.issn2047-217X-
dc.identifier.urihttps://academic.oup.com/gigascience/article/7/7/giy086/5052204-
dc.identifier.urihttp://repository.hanyang.ac.kr/handle/20.500.11754/119384-
dc.description.abstractBackground: 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.en_US
dc.description.sponsorshipThis work was supported by the Cooperative Research Program for Agriculture Science and Technology Development (project title: National Agricultural Genome Program, Project No. PJ01045301 and PJ01045303).en_US
dc.language.isoen_USen_US
dc.publisherOXFORD UNIV PRESSen_US
dc.subjectGallus gallus domesticusen_US
dc.subjectYeonsan Ogyeen_US
dc.subjectwhole genome de novo assemblyen_US
dc.subjecttranscriptome mapsen_US
dc.subjecthyperpigmentationen_US
dc.titleWhole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogyeen_US
dc.typeArticleen_US
dc.relation.no7-
dc.relation.volume7-
dc.identifier.doi10.1093/gigascience/giy086-
dc.relation.page1-14-
dc.relation.journalGIGASCIENCE-
dc.contributor.googleauthorSohn, Jang-il-
dc.contributor.googleauthorNam, Kyoungwoo-
dc.contributor.googleauthorHong, Hyosun-
dc.contributor.googleauthorKim, Jun-Mo-
dc.contributor.googleauthorLim, Dajeong-
dc.contributor.googleauthorLee, Kyung-Tai-
dc.contributor.googleauthorDo, Yoon Jung-
dc.contributor.googleauthorCho, Chang Yeon-
dc.contributor.googleauthorKim, Namshin-
dc.contributor.googleauthorNam, Jin-Wu-
dc.relation.code2018010687-
dc.sector.campusS-
dc.sector.daehakCOLLEGE OF NATURAL SCIENCES[S]-
dc.sector.departmentDEPARTMENT OF LIFE SCIENCE-
dc.identifier.pidjwnam-
dc.identifier.orcidhttp://orcid.org/0000-0003-0047-3687-
Appears in Collections:
COLLEGE OF NATURAL SCIENCES[S](자연과학대학) > LIFE SCIENCE(생명과학과) > Articles
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