Supporting data for "Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye"

Dataset type: Genomic, Transcriptomic, Epigenomic
Data released on July 05, 2018

Sohn J; Nam K; Hong H; Kim J; Lim D; Lee K; Do YJ; Cho CY; Kim N; Chai H; Nam J (2018): Supporting data for "Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye" GigaScience Database. http://dx.doi.org/10.5524/100467

DOI10.5524/100467

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 PacBio long-reads (9.7X). The contig and scaffold NG50s of the hybrid de novo assembly were 362.3Kbp and 16.8Mbp, respectively. The completeness (97.6%) of the draft genome (Ogye_1.1) was evaluated with single copy orthologous genes using BUSCO, 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 5, the draft genome included 551 structural variations including the Fibromelanosis (FM) locus duplication, related to hyperpigmentation. To comprehensively reconstruct transcriptome maps, RNA sequencing (RNA-seq) and reduced representation bisulfite sequencing (RRBS) data were analyzed from twenty different tissues, including four black tissues (skin, shank, comb, and fascia). The maps included 15,766 protein-coding and 6,900 long non-coding RNA genes, many of which were tissue-specifically expressed and displayed tissue-specific DNA methylation patterns in the promoter regions. 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.

Additional details

Accessions (data included in GigaDB):

BioProject: PRJNA412408





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
RNA_19031ChickenGallus gallus Description:Single-end RNA-seq data from Breast of...
Molecular data type:RNA
Tissue:Breast
...
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RNA_109031ChickenGallus gallus Description:Single-end RNA-seq data from Mature eg...
Molecular data type:RNA
Tissue:Mature egg
...
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RNA_119031ChickenGallus gallus Description:Single-end RNA-seq data from Cerebellu...
Molecular data type:RNA
Tissue:Cerebellum
...
+
RNA_129031ChickenGallus gallus Description:Single-end RNA-seq data from Gall blad...
Molecular data type:RNA
Tissue:Gall bladder
...
+
RNA_139031ChickenGallus gallus Description:Single-end RNA-seq data from Kidney of...
Molecular data type:RNA
Tissue:Kidney
...
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RNA_149031ChickenGallus gallus Description:Single-end RNA-seq data from Heart of ...
Molecular data type:RNA
Tissue:Heart
...
+
RNA_159031ChickenGallus gallus Description:Single-end RNA-seq data from Uterus of...
Molecular data type:RNA
Tissue:Uterus
...
+
RNA_169031ChickenGallus gallus Description:Single-end RNA-seq data from Pancreas ...
Molecular data type:RNA
Tissue:Pancreas
...
+
RNA_179031ChickenGallus gallus Description:Single-end RNA-seq data from Lung of t...
Molecular data type:RNA
Tissue:Lung
...
+
RNA_189031ChickenGallus gallus Description:Single-end RNA-seq data from Skin of t...
Molecular data type:RNA
Tissue:Skin
...
+
Displaying 1-10 of 41 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
RRBS_15Methylome dataUNKNOWN0 KB2018-06-26
WGS_YO_02127InDelsVCF0 KB2018-06-26
WGS_YO_02127SNPsVCF0 KB2018-06-26
ReadmeTEXT4.8 KB2018-06-26
Displaying 31-34 of 34 File(s).
Funding body Awardee Award ID Comments
Rural Development Administration Han-Ha Chai PJ01045301 Cooperative Research Program for Agriculture Science and Technology Development
Rural Development Administration Jin-Wu Nam PJ01045303 Cooperative Research Program for Agriculture Science and Technology Development

Protocols.io:

Date Action
July 4, 2018 Dataset publish