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

GigaScience
Jang-Il SohnJin-Wu Nam

Abstract

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). 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, s...Continue Reading

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Citations

Aug 15, 2018·International Journal of Molecular Sciences·Hyosun HongJin-Wu Nam
Sep 30, 2020·Poultry Science·Prabuddha ManjulaJun Heon Lee
May 11, 2021·Mitochondrial DNA. Part B, Resources·Xunhe HuangBingwang Du
May 18, 2021·Frontiers in Genetics·Fergal J MartinPaul Flicek

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Datasets Mentioned

BETA
GSE
104
358
PRJNA412408

Methods Mentioned

BETA
RNA-seq
Illumina sequencing
PCR
RRBS
PCA

Key Resources (RRID) Mentioned

SCR_011848
SCR_010742
SCR_015026
SCR_012091
SCR_001876
SCR_015008
SCR_011980
SCR_012954
SCR_014597

Software Mentioned

ALLPATHS
TSRATOR
GATK
KmerFreq Corrector
VarScan
Opera scaffolder
MUMmer
BWA
FermiKit
rsgcc R package

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