Project description:Assembly of Korean traditional long-tailed chicken and pangenome graph of 40 gallus gallus reveals KLC specific structural variants
Project description:To characterize breed-specific difference among four Korean native chicken breeds and White Leghorn, we measured their transcriptomes at liver tissue using Affymetrix Chicken gene 1.0 ST array platform.
Project description:Macaque species share over 93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them valuable animal models for the study of human diseases (e.g.,HIV and neurodegenerative diseases). However, the quality of genome assembly and annotation for several macaque species lags behind the human genome effort. To close this gap and enhance functional genomics approaches, we employed a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque (Macaca nemestrina) genome. This combinatorial method yielded large scaffolds at chromosome-level with a scaffold N50 of 127.5 Mb; the 23 largest scaffolds covered 90% of the entire genome. This assembly revealed large-scale rearrangements between pig-tailed macaque chromosomes 7, 12, and 13 and human chromosomes 2, 14, and 15. We subsequently annotated the genome using transcriptome and proteomics data from personalized induced pluripotent stem cells (iPSCs) derived from the same animal. Reconstruction of the evolutionary tree using whole genome annotation and orthologous comparisons among three macaque species, human and mouse genomes revealed extensive homology between human and pig-tailed macaques with regards to both pluripotent stem cell genes and innate immune gene pathways. Our results confirm that rhesus and cynomolgus macaques exhibit a closer evolutionary distance to each other than either species exhibits to humans or pig-tailed macaques. These findings demonstrate that pig-tailed macaques can serve as an excellent animal model for the study of many human diseases particularly with regards to pluripotency and innate immune pathways.
Project description:The Yeonsan Ogye (Ogye) is the rare black chicken breed domesticated in Korean peninsula, which has been noted for entire black color upon its appearances including feather, skin, comb, eyes, shank, claws and internal organs. In this study, whole genome, transcriptome and epigenome sequencings of Ogye were performed using high-throughput NGS sequencing platforms. We have produced Illumina short-reads (Paired-End, Mate-Pair and FOSMID) and PacBio long-reads for whole genome sequencing (WGS), 1.4 billion reads for RNA-seq, and 123 million reads for RRBS (reduced representation bisulfite sequencing) data. Using WGS data, Ogye genome has been assembled, and coding/non-coding transcriptome maps were constructed on Ogye genome given largescale sequencing data. We have predicted 17,472 (3,550 newly annotated and 13,922 known) protein-coding transcripts, and 9,443 (6,689 novel and 2,754 known) long non-coding RNAs (lncRNAs).
Project description:The Yeonsan Ogye (Ogye) is the rare black chicken breed domesticated in Korean peninsula, which has been noted for entire black color upon its appearances including feather, skin, comb, eyes, shank, claws and internal organs. In this study, whole genome, transcriptome and epigenome sequencings of Ogye were performed using high-throughput NGS sequencing platforms. We have produced Illumina short-reads (Paired-End, Mate-Pair and FOSMID) and PacBio long-reads for whole genome sequencing (WGS), 1.4 billion reads for RNA-seq, and 123 million reads for RRBS (reduced representation bisulfite sequencing) data. Using WGS data, Ogye genome has been assembled, and coding/non-coding transcriptome maps were constructed on Ogye genome given largescale sequencing data. We have predicted 17,472 (3,550 newly annotated and 13,922 known) protein-coding transcripts, and 9,443 (6,689 novel and 2,754 known) long non-coding RNAs (lncRNAs).
Project description:The Yeonsan Ogye, a culturally significant but small Korean chicken breed has been extensively studied for its fibromelanosis, leaving its low body weight and growth rate relatively unexplored. Here we present the first comparative hepatic transcriptome analysis of Ogye and the heavy, fast-growing Korean Brown Cornish breed at the critical stages of 5 and 10 weeks of age. Using RNA sequencing (RNA-seq) and bioinformatic analyses we uncovered significant and dynamic differences between the breeds. At 5 weeks, Ogye livers exhibited enriched inflammatory and energy-transfer processes (oxidoreductase activity, mitochondrial function), whereas in Cornish livers, translational and macromolecule biosynthesis pathways (ribosomal structure, RNA binding) were enriched. By 10 weeks, Ogye shifts further toward immune- and stimulus-response functions (cytokine/chemokine signaling, MAPK pathway, oxidative phosphorylation), while Cornish maintains elevated protein modification, intracellular transport, and RNA processing activities. Moreover, within the differentially expressed MAPK signaling pathway, genes involved in the regulation of cellular metabolism (FGF19, DUSP8, PTPRR, CACNA1C, CACNA1S, among others) were upregulated in Ogye while growth factor-related genes (IGF1, IGF2, EGFR, VEGFC, and FGFR3) stood out among the Cornish chicken. These patterns suggest contrasting metabolic signatures — a high maintenance, energy expending profile in Ogye versus a growth efficient, anabolic profile in Cornish — and reveal temporal switching of core pathways across development. Consequently, our findings provide a basis for future initiatives aimed at developing biotechnological solutions to enhance growth and weight gain in Ogye and potentially other small chicken breeds.