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_199031ChickenGallus gallus Description:Single-end RNA-seq data from Eye of th...
Molecular data type:RNA
Tissue:Eye
...
+
RNA_29031ChickenGallus gallus Description:Single-end RNA-seq data from Liver of ...
Molecular data type:RNA
Tissue:Liver
...
+
RNA_209031ChickenGallus gallus Description:Single-end RNA-seq data from Shank of ...
Molecular data type:RNA
Tissue:Shank
...
+
RNA_39031ChickenGallus gallus Description:Single-end RNA-seq data from Bone marr...
Molecular data type:RNA
Tissue:Bone marrow
...
+
RNA_49031ChickenGallus gallus Description:Single-end RNA-seq data from Fascia of...
Molecular data type:RNA
Tissue:Fascia
...
+
RNA_59031ChickenGallus gallus Description:Single-end RNA-seq data from Cerebrum ...
Molecular data type:RNA
Tissue:Cerebrum
...
+
RNA_69031ChickenGallus gallus Description:Single-end RNA-seq data from Gizzard o...
Molecular data type:RNA
Tissue:Gizzard
...
+
RNA_79031ChickenGallus gallus Description:Single-end RNA-seq data from Immature ...
Molecular data type:RNA
Tissue:Immature egg
...
+
RNA_89031ChickenGallus gallus Description:Single-end RNA-seq data from Comb of t...
Molecular data type:RNA
Tissue:Comb
...
+
RNA_99031ChickenGallus gallus Description:Single-end RNA-seq data from Spleen of...
Molecular data type:RNA
Tissue:Spleen
...
+
Displaying 11-20 of 41 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
RNA_19 +AnnotationUNKNOWN0 KB2018-06-26
RNA_19 +Expression dataTEXT0 KB2018-06-26
RNA_19 +AnnotationUNKNOWN0 KB2018-06-26
RNA_19 +Sequence assemblyFASTA0 KB2018-06-26
RNA_19 +Sequence assemblyFASTA0 KB2018-06-26
RNA_19 +Expression dataTEXT0 KB2018-06-26
RNA_19 +Expression dataTEXT0 KB2018-06-26
RRBS_19Methylome dataUNKNOWN0 KB2018-06-26
RRBS_20Methylome dataUNKNOWN0 KB2018-06-26
ReadmeTEXT4.8 KB2018-06-26
Displaying 1-10 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