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Horecka B, Wojciechowski W, Drabik K, Wengerska K, Batkowska J. Characterization of the Coding Sequence of the MC1R (Melanocortin 1 Receptor) Gene of Ayam Cemani Black Chickens. Animals (Basel) 2024; 14:2507. [PMID: 39272291 PMCID: PMC11394068 DOI: 10.3390/ani14172507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 08/21/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024] Open
Abstract
Plumage color is one of the most important traits characterizing chicken breeds. Black-boned chickens constitute a specific group of breeds with a unique phenotype. One of the representatives is the Indonesian Ayam Cemani. The extraordinary black phenotype results from a specific chromosomal rearrangement. We used complete CDS of crucial color-related gene MC1R, which plays a key role in melanin distribution but has not been previously studied in Ayam Cemani. It turned out that Ayam Cemani individuals possess a newly found non-synonymous mutation G355A resulting in amino acid substitution D119N. Together with the presence of G274A (E92K), the new missense variant enabled us to distinguish a new extended black allele at the E locus. All of the investigated birds were heterozygous in terms of the new mutation. Previous studies and our own results indicate a high level of genetic variation within the MC1R gene within and between chicken breeds. Besides the key mutations that make it possible to distinguish particular major alleles, there are also numerous substitutions that give haplotypes more characteristics for individual breeds.
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Affiliation(s)
- Beata Horecka
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Witold Wojciechowski
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Kamil Drabik
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Karolina Wengerska
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Justyna Batkowska
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland
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2
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Cha J, Jin D, Kim JH, Kim SC, Lim JA, Chai HH, Jung SA, Lee JH, Lee SH. Genome-wide association study revealed the genomic regions associated with skin pigmentation in an Ogye x White Leghorn F2 chicken population. Poult Sci 2023; 102:102720. [PMID: 37327746 PMCID: PMC10404675 DOI: 10.1016/j.psj.2023.102720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 06/18/2023] Open
Abstract
Skin color in chickens is an economically important trait that determines the first impression of a consumer toward a broiler and can ultimately affect consumer choice in the market. Therefore, identification of genomic regions associated with skin color is crucial for increasing the sales value of chickens. Although previous studies have attempted to reveal the genetic markers associated with the skin coloration in chickens, most were limited to investigations of candidate genes, such as melanin-related genes, and focused on case/control studies based on a single or small population. In this study, we performed a genome-wide association study (GWAS) on 770 F2 intercrosses produced by an experimental population of 2 chicken breeds, namely Ogye and White Leghorns, with different skin colors. The GWAS demonstrated that the L* value among the 3 skin color traits is highly heritable, and the genomic regions located on 2 chromosomes (20 and Z) were detected to harbor SNPs significantly associated with the skin color trait, accounting for most of the total genetic variance. Particular genomic regions spanning a ∼2.94 Mb region on GGA Z and a ∼3.58 Mb region on GGA 20 were significantly associated with skin color traits, and in these regions, certain candidate genes, including MTAP, FEM1C, GNAS, and EDN3, were found. Our findings could help elucidate the genetic mechanisms underlying chicken skin pigmentation. Furthermore, the candidate genes can be used to provide a valuable breeding strategy for the selection of specific chicken breeds with ideal skin coloration.
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Affiliation(s)
- Jihye Cha
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Daehyeok Jin
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, South Korea
| | - Jae-Hwan Kim
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Seung-Chang Kim
- Animal Genetic Resources Research Center, National Institute of Animal Science, Rural Development Administration, Hamyang 50000, South Korea
| | - Jin A Lim
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Han-Ha Chai
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Seul A Jung
- Animal Genome & Bioinformatics, National Institute of Animal Science, Rural Development Administration, Wanju 55365, South Korea
| | - Jun-Heon Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, South Korea
| | - Seung-Hwan Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 34134, South Korea.
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3
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Shinde SS, Sharma A, Vijay N. Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken. Front Genet 2023; 14:1180658. [PMID: 37424723 PMCID: PMC10325862 DOI: 10.3389/fgene.2023.1180658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023] Open
Abstract
Black-bone chicken (BBC) meat is popular for its distinctive taste and texture. A complex chromosomal rearrangement at the fibromelanosis (Fm) locus on the 20th chromosome results in increased endothelin-3 (EDN3) gene expression and is responsible for melanin hyperpigmentation in BBC. We use public long-read sequencing data of the Silkie breed to resolve high-confidence haplotypes at the Fm locus spanning both Dup1 and Dup2 regions and establish that the Fm_2 scenario is correct of the three possible scenarios of the complex chromosomal rearrangement. The relationship between Chinese and Korean BBC breeds with Kadaknath native to India is underexplored. Our data from whole-genome re-sequencing establish that all BBC breeds, including Kadaknath, share the complex chromosomal rearrangement junctions at the fibromelanosis (Fm) locus. We also identify two Fm locus proximal regions (∼70 Kb and ∼300 Kb) with signatures of selection unique to Kadaknath. These regions harbor several genes with protein-coding changes, with the bactericidal/permeability-increasing-protein-like gene having two Kadaknath-specific changes within protein domains. Our results indicate that protein-coding changes in the bactericidal/permeability-increasing-protein-like gene hitchhiked with the Fm locus in Kadaknath due to close physical linkage. Identifying this Fm locus proximal selective sweep sheds light on the genetic distinctiveness of Kadaknath compared to other BBC.
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Affiliation(s)
| | | | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
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4
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The study of selection signature and its applications on identification of candidate genes using whole genome sequencing data in chicken - a review. Poult Sci 2023; 102:102657. [PMID: 37054499 PMCID: PMC10123265 DOI: 10.1016/j.psj.2023.102657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Chicken is a major source of protein for the increasing human population and is useful for research purposes. There are almost 1,600 distinct regional breeds of chicken across the globe, among which a large body of genetic and phenotypic variations has been accumulated due to extensive natural and artificial selection. Moreover, natural selection is a crucial force for animal domestication. Several approaches have been adopted to detect selection signatures in different breeds of chicken using whole genome sequencing (WGS) data including integrated haplotype score (iHS), cross-populated extend haplotype homozygosity test (XP-EHH), fixation index (FST), cross-population composite likelihood ratio (XP-CLR), nucleotide diversity (Pi), and others. In addition, gene enrichment analyses are utilized to determine KEGG pathways and gene ontology (GO) terms related to traits of interest in chicken. Herein, we review different studies that have adopted diverse approaches to detect selection signatures in different breeds of chicken. This review systematically summarizes different findings on selection signatures and related candidate genes in chickens. Future studies could combine different selection signatures approaches to strengthen the quality of the results thereby providing more affirmative inference. This would further aid in deciphering the importance of selection in chicken conservation for the increasing human population.
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Kasianov AS, Klepikova AV, Mayorov AV, Buzanov GS, Logacheva MD, Penin AA. Interspecific comparison of gene expression profiles using machine learning. PLoS Comput Biol 2023; 19:e1010743. [PMID: 36626392 PMCID: PMC9879537 DOI: 10.1371/journal.pcbi.1010743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/26/2023] [Accepted: 11/16/2022] [Indexed: 01/11/2023] Open
Abstract
Interspecific gene comparisons are the keystones for many areas of biological research and are especially important for the translation of knowledge from model organisms to economically important species. Currently they are hampered by the low resolution of methods based on sequence analysis and by the complex evolutionary history of eukaryotic genes. This is especially critical for plants, whose genomes are shaped by multiple whole genome duplications and subsequent gene loss. This requires the development of new methods for comparing the functions of genes in different species. Here, we report ISEEML (Interspecific Similarity of Expression Evaluated using Machine Learning)-a novel machine learning-based algorithm for interspecific gene classification. In contrast to previous studies focused on sequence similarity, our algorithm focuses on functional similarity inferred from the comparison of gene expression profiles. We propose novel metrics for expression pattern similarity-expression score (ES)-that is suitable for species with differing morphologies. As a proof of concept, we compare detailed transcriptome maps of Arabidopsis thaliana, the model species, Zea mays (maize) and Fagopyrum esculentum (common buckwheat), which are species that represent distant clades within flowering plants. The classifier resulted in an AUC of 0.91; under the ES threshold of 0.5, the specificity was 94%, and sensitivity was 72%.
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Affiliation(s)
- Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Mayorov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | | | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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6
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Cho Y, Kim JY, Kim N. Comparative genomics and selection analysis of Yeonsan Ogye black chicken with whole-genome sequencing. Genomics 2022; 114:110298. [PMID: 35134497 DOI: 10.1016/j.ygeno.2022.110298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/24/2021] [Accepted: 02/01/2022] [Indexed: 11/30/2022]
Abstract
Yeonsan Ogye (OGYE; Gallus gallus domesticus) is a rare indigenous chicken breed that inhabits the Korean Peninsula. This breed has completely black coloring, including plumage, skin, eyes, beak, and internal organs. Despite these unique morphological characteristics, the population of OGYE has declined without in-depth research into their genome research. Therefore, this study aimed to compare the whole genome of OGYE to 12 other chicken populations, including ancestral breed, commercial breeds, Chinese indigenous breeds, and Korean native chickens. We focused on revealing the selection signature of OGYE, which has occurred through environmental pressures in the Korean Peninsula. Genome-wide selection analysis has identified local adaptation traits, such as egg development, that contribute to fetal viability and innate immune response to prevent viral and microbes infection in OGYE. In particular, SPP1 (Secreted Phosphoprotein 1), HSP90AA1 (Heat Shock Protein 90 Alpha Family Class A Member 1), and P2RX4 (Purinergic Receptor P2X 4) could have considerable involvement in egg development and RNASEL (Ribonuclease L), BRIP1 (BRCA1 Interacting Protein C-terminal Helicase 1), and TLR4 (Toll-Like Receptor 4) are crucial for the determination of the innate immune response. This study revealed the unique genetic diversity of OGYE at the genome-wide level. Furthermore, we emphasized the sustainable management of genetic resources and formulated breeding strategies for livestock on the Korean Peninsula.
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Affiliation(s)
- Youngbeom Cho
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea.
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7
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Martin FJ, Gall A, Szpak M, Flicek P. Accessing Livestock Resources in Ensembl. Front Genet 2021; 12:650228. [PMID: 33995484 PMCID: PMC8115729 DOI: 10.3389/fgene.2021.650228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/18/2021] [Indexed: 12/12/2022] Open
Abstract
Genome assembly is cheaper, more accurate and more automated than it has ever been. This is due to a combination of more cost-efficient chemistries, new sequencing technologies and better algorithms. The livestock community has been at the forefront of this new wave of genome assembly, generating some of the highest quality vertebrate genome sequences. Ensembl's goal is to add functional and comparative annotation to these genomes, through our gene annotation, genomic alignments, gene trees, regulatory, and variation data. We run computationally complex analyses in a high throughput and consistent manner to help accelerate downstream science. Our livestock resources are continuously growing in both breadth and depth. We annotate reference genome assemblies for newly sequenced species and regularly update annotation for existing genomes. We are the only major resource to support the annotation of breeds and other non-reference assemblies. We currently provide resources for 13 pig breeds, maternal and paternal haplotypes for hybrid cattle and various other non-reference or wild type assemblies for livestock species. Here, we describe the livestock data present in Ensembl and provide protocols for how to view data in our genome browser, download via it our FTP site, manipulate it via our tools and interact with it programmatically via our REST API.
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Affiliation(s)
- Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Michal Szpak
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
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8
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Huang X, Weng Z, He Y, Miao Y, Luo W, Zhang X, Zhong F, Du B. Mitochondrial DNA diversity and demographic history of Black-boned chickens in China. Mitochondrial DNA B Resour 2021; 6:1462-1467. [PMID: 33969196 PMCID: PMC8079009 DOI: 10.1080/23802359.2021.1912668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/29/2021] [Indexed: 11/30/2022] Open
Abstract
Black-boned chickens (Gallus domesticus, herein abbreviated BBCs) are well known for their unique appearance and medicinal properties and have a long breeding history in China. However, the genetic diversity and demographic history of BBCs remain unclear. In this study, we analyzed 844 mitochondrial DNA D-loop sequences, including 346 de novo sequences and 498 previously published sequences from 20 BBC breeds. We detected a generally high level of genetic diversity among the BBCs, with average haplotype and nucleotide diversities of 0.917 ± 0.0049 and 0.01422, respectively. Nucleotide diversity was highest in populations from Southwest China (0.01549 ± 0.00026), particularly in Yunnan Province (0.01624 ± 0.00025). Significant genetic divergence was detected between most breeds, particularly between Yunnan chickens and those from all other provinces. Haplogroups F and G had the highest levels of genetic diversity and were restricted to Southwest China, particularly Yunnan Province. Based on neutrality tests and mismatch distribution analyses, we did not obtain evidence for rapid population expansions and observed similar demographic histories in BBCs and local non-BBCs. Our results suggest that Chinese BBCs have complex breeding histories and may be selected in situ from local domestic chickens. These results improve our understanding of the genetic heritage and breeding histories of these desirable chickens.
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Affiliation(s)
- Xunhe Huang
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
| | - Zhuoxian Weng
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
- College of Animal Science and Technology, Hunan Agricultural University,Changsha, China
| | - Yujing He
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
| | - Yongwang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Wei Luo
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiquan Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Fusheng Zhong
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
- College of Animal Science and Technology, Hunan Agricultural University,Changsha, China
| | - Bingwang Du
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
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9
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Manjula P, Fulton JE, Seo D, Lee JH. Major histocompatibility complex B variability in Korean native chicken breeds. Poult Sci 2020; 99:4704-4713. [PMID: 32988505 PMCID: PMC7598131 DOI: 10.1016/j.psj.2020.05.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/04/2020] [Accepted: 05/22/2020] [Indexed: 12/01/2022] Open
Abstract
Adaptive genetic variations have direct influences on the fitness traits of the animal. The major histocompatibility complex B (MHC-B) region is responsible for adaptive and innate immune responses in chickens. In native Korean chicken breeds, no information on serologically defined B haplotypes is available. We investigated the MHC-B diversity in 5 restored lines of Korean native chicken and Ogye chicken breeds using a recently described MHC-B single-nucleotide polymorphism (SNP) panel and the MHC-linked LEI0258 variable number of tandem repeat marker. High SNP haplotype diversity was observed in Korean native chicken breeds with an average of 9.7 MHC-B SNP haplotypes per line. The total number of haplotypes ranged from 6 to 12 per line, and population-specific haplotypes ranged from 3 to 4. A total of 41 BSNP haplotypes, including 26 novel population-specific haplotypes and 15 common haplotypes, were reported over all populations. The 15 common haplotypes included 7 novel and 8 previously reported standard haplotypes. Selection and breeding evidence supports the observation of common haplotypes between the Korean native chicken and exotic breeds. Similarly, the LEI0258 marker showed allele variation, between 193 bp and 474 bp having 5 to 8 alleles per population. Some of these alleles (193, 249, 309, and 443 bp) were shared and more frequently observed. Comparison between SNP haplotypes and LEI0258 allele sizes for the same samples showed that some LEI0258 allele sizes correspond to more than one BSNP haplotype. The use of the MHC-B SNP panel greatly enhances the identification of MHC diversity compared with the sole use of the LEI0258 marker in native chicken populations.
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Affiliation(s)
- Prabuddha Manjula
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | | | - Dongwon Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea.
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10
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Li D, Sun G, Zhang M, Cao Y, Zhang C, Fu Y, Li F, Li G, Jiang R, Han R, Li Z, Wang Y, Tian Y, Liu X, Li W, Kang X. Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken. BMC Genomics 2020; 21:511. [PMID: 32703156 PMCID: PMC7376702 DOI: 10.1186/s12864-020-06900-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022] Open
Abstract
Background Domesticated chickens have a wide variety of phenotypes, in contrast with their wild progenitors. Unlike other chicken breeds, Xichuan black-bone chickens have blue-shelled eggs, and black meat, beaks, skin, bones, and legs. The breeding history and the economically important traits of this breed have not yet been explored at the genomic level. We therefore used whole genome resequencing to analyze the breeding history of the Xichuan black-bone chickens and to identify genes responsible for its unique phenotype. Results Principal component and population structure analysis showed that Xichuan black-bone chicken is in a distinct clade apart from eight other breeds. Linkage disequilibrium analysis showed that the selection intensity of Xichuan black-bone chickens is higher than for other chicken breeds. The estimated time of divergence between the Xichuan black-bone chickens and other breeds is 2.89 ka years ago. Fst analysis identified a selective sweep that contains genes related to melanogenesis. This region is probably associated with the black skin of the Xichuan black-bone chickens and may be the product of long-term artificial selection. A combined analysis of genomic and transcriptomic data suggests that the candidate gene related to the black-bone trait, EDN3, might interact with the upstream ncRNA LOC101747896 to generate black skin color during melanogenesis. Conclusions These findings help explain the unique genetic and phenotypic characteristics of Xichuan black-bone chickens, and provide basic research data for studying melanin deposition in animals.
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Affiliation(s)
- Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Meng Zhang
- The First Hospital, Jilin University, Changchun, 130062, Jilin, China
| | - Yanfang Cao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Chenxi Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yawei Fu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Fang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Ruirui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Yanbin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China. .,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China.
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11
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Collagen Extract Derived from Yeonsan Ogye Chicken Increases Bone Microarchitecture by Suppressing the RANKL/OPG Ratio via the JNK Signaling Pathway. Nutrients 2020; 12:nu12071967. [PMID: 32630655 PMCID: PMC7400104 DOI: 10.3390/nu12071967] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/21/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
Yeonsan Ogye is a traditional Korean chicken breed (Gallus domesticus, GD), with a dominant gene for fibromelanosis, showing entirely black fluffy head feathers, ear lobes, and pupils. GD collagen extract (78.6 g per 100 g total protein) was derived from the flesh of Yeonsan Ogye. The effects of GD collagen on bone mass, microarchitecture, osteogenic, osteoclastogenic differentiations, and function factor expression were investigated in ovariectomized (OVX) rats. GD collagen stimulated osteogenesis in OVX rats and increased tibial bone strength and calcium content. Micro-computed tomography analysis of tibia cross-sections revealed that GD collagen attenuated the OVX-induced changes in trabecular thickness, spacing, and number. GD collagen stimulated alkaline phosphatase activity, bone-specific matrix proteins (alkaline phosphatase (ALP), osteocalcin, collagen type I (COL-I)) and mineralization by activating bone morphogenetic protein 2 (BMP-2)/mothers against decapentaplegic homolog 5 (SMAD5)/runt-related transcription factor 2 (Runx2). GD collagen inhibited osteoclast differentiation and function gene markers (TRAP, cathepsin K) by interfering with the Wnt signaling, increasing OPG production, and reducing the expression of RANKL, TRAP, and cathepsin K. GD collagen promoted osteogenesis by activating the p38 signal pathway and prevented osteoclastogenesis by lowering the RANKL/OPG ratio and blocking the JNK signaling pathway. Dietary supplementation with GD collagen might inhibit osteoclastogenesis, stimulate osteoblastogenesis, and regulate bone metabolism.
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12
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Peng J, Li Q, Xu L, Wei P, He P, Zhang X, Zhang L, Guan J, Zhang X, Lin Y, Gui J, Chen X. Chromosome-level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune-related genes in bivalves. Mol Ecol Resour 2020; 20:980-994. [PMID: 32198971 DOI: 10.1111/1755-0998.13157] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 03/09/2020] [Accepted: 03/16/2020] [Indexed: 12/30/2022]
Abstract
Crassostrea hongkongensis is a popular and important native oyster species that is cultured mainly along the coast of the South China Sea. However, the absence of a reference genome has restricted genetic studies and the development of molecular breeding schemes for this species. Here, we combined PacBio and 10 × Genomics technologies to create a C. hongkongensis genome assembly, which has a size of 610 Mb, and is close to that estimated by flow cytometry (~650 Mb). Contig and scaffold N50 are 2.57 and 4.99 Mb, respectively, and BUSCO analysis indicates that 95.8% of metazoan conserved genes are completely represented. Using a high-density linkage map of its closest related species, C. gigas, a total of 521 Mb (85.4%) was anchored to 10 haploid chromosomes. Comparative genomic analyses with other molluscs reveal that several immune- or stress response-related genes extensively expanded in bivalves by tandem duplication, including C1q, Toll-like receptors and Hsp70, which are associated with their adaptation to filter-feeding and sessile lifestyles in shallow sea and/or deep-sea ecosystems. Through transcriptome sequencing, potential genes and pathways related to sex determination and gonad development were identified. The genome and transcriptome of C. hongkongensis provide valuable resources for future molecular studies, genetic improvement and genome-assisted breeding of oysters.
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Affiliation(s)
- Jinxia Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Qiongzhen Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Lian Xu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Pinyuan Wei
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Pingping He
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Xingzhi Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Li Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Junliang Guan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Xiaojuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology and Innovation Academy for Seed Design, CAS, Wuhan, China
| | - Yong Lin
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
| | - Jianfang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology and Innovation Academy for Seed Design, CAS, Wuhan, China
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fisheries Sciences, Nanning, China
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A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae). DIVERSITY-BASEL 2019. [DOI: 10.3390/d11090144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Current generation high-throughput sequencing technology has facilitated the generation of more genomic-scale data than ever before, thus greatly improving our understanding of avian biology across a range of disciplines. Recent developments in linked-read sequencing (Chromium 10×) and reference-based whole-genome assembly offer an exciting prospect of more accessible chromosome-level genome sequencing in the near future. We sequenced and assembled a genome of the Hairy-crested Antbird (Rhegmatorhina melanosticta), which represents the first publicly available genome for any antbird (Thamnophilidae). Our objectives were to (1) assemble scaffolds to chromosome level based on multiple reference genomes, and report on differences relative to other genomes, (2) assess genome completeness and compare content to other related genomes, and (3) assess the suitability of linked-read sequencing technology for future studies in comparative phylogenomics and population genomics studies. Our R. melanosticta assembly was both highly contiguous (de novo scaffold N50 = 3.3 Mb, reference based N50 = 53.3 Mb) and relatively complete (contained close to 90% of evolutionarily conserved single-copy avian genes and known tetrapod ultraconserved elements). The high contiguity and completeness of this assembly enabled the genome to be successfully mapped to the chromosome level, which uncovered a consistent structural difference between R. melanosticta and other avian genomes. Our results are consistent with the observation that avian genomes are structurally conserved. Additionally, our results demonstrate the utility of linked-read sequencing for non-model genomics. Finally, we demonstrate the value of our R. melanosticta genome for future researchers by mapping reduced representation sequencing data, and by accurately reconstructing the phylogenetic relationships among a sample of thamnophilid species.
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Mukherjee S, Cai Z, Mukherjee A, Longkumer I, Mech M, Vupru K, Khate K, Rajkhowa C, Mitra A, Guldbrandtsen B, Lund MS, Sahana G. Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis). BMC Genomics 2019; 20:617. [PMID: 31357931 PMCID: PMC6664528 DOI: 10.1186/s12864-019-5980-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/16/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Mithun (Bos frontalis), also called gayal, is an endangered bovine species, under the tribe bovini with 2n = 58 XX chromosome complements and reared under the tropical rain forests region of India, China, Myanmar, Bhutan and Bangladesh. However, the origin of this species is still disputed and information on its genomic architecture is scanty so far. We trust that availability of its whole genome sequence data and assembly will greatly solve this problem and help to generate many information including phylogenetic status of mithun. Recently, the first genome assembly of gayal, mithun of Chinese origin, was published. However, an improved reference genome assembly would still benefit in understanding genetic variation in mithun populations reared under diverse geographical locations and for building a superior consensus assembly. We, therefore, performed deep sequencing of the genome of an adult female mithun from India, assembled and annotated its genome and performed extensive bioinformatic analyses to produce a superior de novo genome assembly of mithun. RESULTS We generated ≈300 Gigabyte (Gb) raw reads from whole-genome deep sequencing platforms and assembled the sequence data using a hybrid assembly strategy to create a high quality de novo assembly of mithun with 96% recovered as per BUSCO analysis. The final genome assembly has a total length of 3.0 Gb, contains 5,015 scaffolds with an N50 value of 1 Mb. Repeat sequences constitute around 43.66% of the assembly. The genomic alignments between mithun to cattle showed that their genomes, as expected, are highly conserved. Gene annotation identified 28,044 protein-coding genes presented in mithun genome. The gene orthologous groups of mithun showed a high degree of similarity in comparison with other species, while fewer mithun specific coding sequences were found compared to those in cattle. CONCLUSION Here we presented the first de novo draft genome assembly of Indian mithun having better coverage, less fragmented, better annotated, and constitutes a reasonably complete assembly compared to the previously published gayal genome. This comprehensive assembly unravelled the genomic architecture of mithun to a great extent and will provide a reference genome assembly to research community to elucidate the evolutionary history of mithun across its distinct geographical locations.
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Affiliation(s)
- Sabyasachi Mukherjee
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Zexi Cai
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Anupama Mukherjee
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
- Present address: Dairy Cattle Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
| | - Imsusosang Longkumer
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Moonmoon Mech
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Kezhavituo Vupru
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Kobu Khate
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Chandan Rajkhowa
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Abhijit Mitra
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
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15
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Lim WJ, Kim KH, Kim JY, Jeong S, Kim N. Identification of DNA-Methylated CpG Islands Associated With Gene Silencing in the Adult Body Tissues of the Ogye Chicken Using RNA-Seq and Reduced Representation Bisulfite Sequencing. Front Genet 2019; 10:346. [PMID: 31040866 PMCID: PMC6476954 DOI: 10.3389/fgene.2019.00346] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/01/2019] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is an epigenetic mark that plays an essential role in regulating gene expression. CpG islands are DNA methylations regions in promoters known to regulate gene expression through transcriptional silencing of the corresponding gene. DNA methylation at CpG islands is crucial for gene expression and tissue-specific processes. At the current time, a limited number of studies have reported on gene expression associated with DNA methylation in diverse adult tissues at the genome-wide level. Expression levels are rarely affected by DNA methylation in normal adult tissues; however, statistical differences in gene expression level correlated with DNA methylation have recently been revealed. In this study, we examined 20 pairs of DNA methylomes and transcriptomes from RNA-seq and reduced representation bisulfite sequencing (RRBS) data using adult Ogye chicken tissues. A total of 3,133 CpG islands were identified from 20 tissue data in a single chicken sample which could affect downstream genes. Analyzing these CpG island and gene pairs, 121 significant units were statistically correlated. Among them, six genes (CLDN3, DECR2, EVA1B, NME4, NTSR1, and XPNPEP2) were highly significantly changed by altered DNA methylation. Finally, our data demonstrated how DNA methylation correlated to gene expression in normal adult tissues. Our source codes can be found at https://github.com/wjlim/correlation-between-rna-seq-and-RRBS.
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Affiliation(s)
- Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, South Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, South Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, South Korea
| | - Seongmun Jeong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, South Korea
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16
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Hong H, Chai HH, Nam K, Lim D, Lee KT, Do YJ, Cho CY, Nam JW. Non-Coding Transcriptome Maps across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye. Int J Mol Sci 2018; 19:ijms19082359. [PMID: 30103450 PMCID: PMC6121550 DOI: 10.3390/ijms19082359] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 07/15/2018] [Accepted: 08/08/2018] [Indexed: 12/14/2022] Open
Abstract
Yeonsan Ogye is a rare Korean domestic chicken breed whose entire body, including feathers and skin, has a unique black coloring. Although some protein-coding genes related to this unique feature have been examined, non-coding elements have not been widely investigated. Thus, we evaluated coding and non-coding transcriptome expression and identified long non-coding RNAs functionally linked to protein-coding genes in Ogye. High-throughput RNA sequencing and DNA methylation sequencing were performed to profile the expression of 14,264 Ogye protein-coding and 6900 long non-coding RNA (lncRNA) genes and detect DNA methylation in 20 different tissues of an individual Ogye. Approximately 75% of Ogye lncRNAs and 45% of protein-coding genes showed tissue-specific expression. For some genes, tissue-specific expression levels were inversely correlated with DNA methylation levels in their promoters. Approximately 39% of tissue-specific lncRNAs displayed functional associations with proximal or distal protein-coding genes. Heat shock transcription factor 2-associated lncRNAs appeared to be functionally linked to protein-coding genes specifically expressed in black skin tissues, more syntenically conserved in mammals, and differentially expressed in black relative to in white tissues. Pending experimental validation, our findings increase the understanding of how the non-coding genome regulates unique phenotypes and can be used for future genomic breeding of chickens.
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Affiliation(s)
- Hyosun Hong
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Korea.
| | - Han-Ha Chai
- Department of Animal Biotechnology & Environment of National Institute of Animal Science, RDA, Wanju 55365, Korea.
- College of Pharmacy, Chonnam National University, Kwangju 61186, Korea.
| | - Kyoungwoo Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Korea.
| | - Dajeong Lim
- Department of Animal Biotechnology & Environment of National Institute of Animal Science, RDA, Wanju 55365, Korea.
| | - Kyung-Tai Lee
- Department of Animal Biotechnology & Environment of National Institute of Animal Science, RDA, Wanju 55365, Korea.
| | - Yoon Jung Do
- Department of Animal Biotechnology & Environment of National Institute of Animal Science, RDA, Wanju 55365, Korea.
| | - Chang-Yeon Cho
- Animal Genetic Resource Research Center of National Institute of Animal Science, RDA, Namwon 55717, Korea.
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 133791, Korea.
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17
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Sohn JI, Nam K, Hong H, Kim JM, Lim D, Lee KT, Do YJ, Cho CY, Kim N, Chai HH, Nam JW. Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye. Gigascience 2018; 7:5052204. [PMID: 30010758 PMCID: PMC6065499 DOI: 10.1093/gigascience/giy086] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/19/2018] [Accepted: 07/04/2018] [Indexed: 12/30/2022] Open
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). Findings 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, 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. Conclusions 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.
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Affiliation(s)
- Jang-il Sohn
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Kyoungwoo Nam
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Hyosun Hong
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Dajeong Lim
- Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Kyung-Tai Lee
- Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Yoon Jung Do
- Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Chang Yeon Cho
- Animal Genetic Resource Research Center, National Institute of Animal Science, RDA, Namwon, 55717, Republic of Korea
| | - Namshin Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Han-Ha Chai
- Department of Animal Biotechnology & Environment, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
- College of Pharmacy, Chonnam National University, Kwangju, 61186, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 133-791, Republic of Korea
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