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

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).FindingsThe 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.ConclusionsWe 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.

Non-Coding Transcriptome Maps across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye

“…Of the 6900 Ogye lncRNAs that we annotated in our previous study [55], 6565 were expressed with fragments per kilobase of transcript per million mapped reads (FPKM) ≥ 1 in at least one tissue, whereas 13,765 of Ensembl chicken protein-coding genes (release 81; ) were expressed. Tissue-specific genes with a four-fold higher maximum expression value than the mean value over the 20 tissues were depicted in the genome using a Circos plot (Supplementary Figure S1a, green track).…”

Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken

“…Recent research has shown that the Fm phenotype (associated with the Fm region) is related to domestication and has been intensely artificially selected, with about 1.5-folder blacker level [ 48 ]. A previous study found that an inverted duplication affecting EDN3 , a key gene in dermal melanin located on chromosome 20 in the Fm region, caused excessive accumulation of black pigment in chickens [ 54 , 55 ]. We also detected an inversion at 10.97–11.52 Mb and a duplication at 10.74–12.55 Mb in EDN3 , which overlaps the Fm region.…”

Chromosome‐level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune‐related genes in bivalves

“…The C. hongkongensis gills (~20 mg) were homogenized and fixed in 1,000 µl of cold 70% ethanol for 15 min at 4°C. Chicken (Gallus gallus, 1.02 Gb; Sohn et al, 2018) red blood cells (RBCs; standard sample) were used as internal reference to estimate C. hongkongensis DNA content. The fixed gill cells and 10 µl chicken RBCs were mixed and then stained with 0.2 ml of propidium iodide (PI) solution (Solarbio) (100 μg/ml DNase-free RNase A [TakaRa], 500 μg/ ml PI dye in PBS) was added followed by incubation in the dark for 15 min.…”