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Zhu F, Yin ZT, Zhao QS, Sun YX, Jie YC, Smith J, Yang YZ, Burt DW, Hincke M, Zhang ZD, Yuan MD, Kaufman J, Sun CJ, Li JY, Shao LW, Yang N, Hou ZC. A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes. Commun Biol 2023; 6:1233. [PMID: 38057566 PMCID: PMC10700341 DOI: 10.1038/s42003-023-05619-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
A set of high-quality pan-genomes would help identify important genes that are still hidden/incomplete in bird reference genomes. In an attempt to address these issues, we have assembled a de novo chromosome-level reference genome of the Silkie (Gallus gallus domesticus), which is an important avian model for unique traits, like fibromelanosis, with unclear genetic foundation. This Silkie genome includes the complete genomic sequences of well-known, but unresolved, evolutionarily, endocrinologically, and immunologically important genes, including leptin, ovocleidin-17, and tumor-necrosis factor-α. The gap-less and manually annotated MHC (major histocompatibility complex) region possesses 38 recently identified genes, with differentially regulated genes recovered in response to pathogen challenges. We also provide whole-genome methylation and genetic variation maps, and resolve a complex genetic region that may contribute to fibromelanosis in these animals. Finally, we experimentally show leptin binding to the identified leptin receptor in chicken, confirming an active leptin ligand-receptor system. The Silkie genome assembly not only provides a rich data resource for avian genome studies, but also lays a foundation for further functional validation of resolved genes.
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Affiliation(s)
- Feng Zhu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Zhong-Tao Yin
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Qiang-Sen Zhao
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Yun-Xiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Yu-Chen Jie
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Jacqueline Smith
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Yu-Ze Yang
- Beijing General Station of Animal Husbandry, 100101, Beijing, China
| | - David W Burt
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Maxwell Hincke
- Department of Cellular and Molecular Medicine, Department of Innovation in Medical Education, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, KIH 8M5, Canada
| | - Zi-Ding Zhang
- College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Meng-Di Yuan
- College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Jim Kaufman
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Cong-Jiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Jun-Ying Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China
| | - Li-Wa Shao
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China.
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China.
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100193, Beijing, China.
- Sanya Institute of China Agricultural University, Beijing, China.
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Dascalu S, Preston SG, Dixon RJ, Flammer PG, Fiddaman S, Boyd A, Sealy JE, Sadeyen JR, Kaspers B, Velge P, Iqbal M, Bonsall MB, Smith AL. The influences of microbial colonisation and germ-free status on the chicken TCRβ repertoire. Front Immunol 2023; 13:1052297. [PMID: 36685492 PMCID: PMC9847582 DOI: 10.3389/fimmu.2022.1052297] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/06/2022] [Indexed: 01/06/2023] Open
Abstract
Microbial colonisation is paramount to the normal development of the immune system, particularly at mucosal sites. However, the relationships between the microbiome and the adaptive immune repertoire have mostly been explored in rodents and humans. Here, we report a high-throughput sequencing analysis of the chicken TCRβ repertoire and the influences of microbial colonisation on tissue-resident TCRβ+ cells. The results reveal that the microbiome is an important driver of TCRβ diversity in both intestinal tissues and the bursa of Fabricius, but not in the spleen. Of note, public TCRβ sequences (shared across individuals) make a substantial contribution to the repertoire. Additionally, different tissues exhibit biases in terms of their V family and J gene usage, and these effects were influenced by the gut-associated microbiome. TCRβ clonal expansions were identified in both colonised and germ-free birds, but differences between the groups were indicative of an influence of the microbiota. Together, these findings provide an insight into the avian adaptive immune system and the influence of the microbiota on the TCRβ repertoire.
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Affiliation(s)
- Stefan Dascalu
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Avian Influenza Research Group, The Pirbright Institute, Pirbright, United Kingdom
| | - Stephen G. Preston
- Department of Biology, University of Oxford, Oxford, United Kingdom
- UCL School of Pharmacy, University College London, London, United Kingdom
| | - Robert J. Dixon
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | | | - Steven Fiddaman
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Amy Boyd
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Joshua E. Sealy
- Avian Influenza Research Group, The Pirbright Institute, Pirbright, United Kingdom
| | - Jean-Remy Sadeyen
- Avian Influenza Research Group, The Pirbright Institute, Pirbright, United Kingdom
| | - Bernd Kaspers
- Veterinary Faculty, Ludwig Maximillians University of Munich, Planegg, Germany
| | - Philippe Velge
- Institut National de la Recherche Agronomique (INRAE), Université François Rabelais de Tours, Unités Mixtes de Recherche, Infectiologie et Santé Publique (ISP), Nouzilly, France
| | - Munir Iqbal
- Avian Influenza Research Group, The Pirbright Institute, Pirbright, United Kingdom
| | | | - Adrian L. Smith
- Department of Biology, University of Oxford, Oxford, United Kingdom
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Ediriweera TK, Manjula P, Cho E, Kim M, Lee JH. Application of next-generation sequencing for the high-resolution typing of MHC-B in Korean native chicken. Front Genet 2022; 13:886376. [DOI: 10.3389/fgene.2022.886376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022] Open
Abstract
The major histocompatibility complex-B (MHC-B) region of chicken is crucially important in their immunogenesis and highly diverse among different breeds, lines, and even populations. Because it determines the resistance/susceptibility to numerous infectious diseases, it is important to analyze this genomic region, particularly classical class I and II genes, to determine the variation and diversity that ultimately affect antigen presentation. This study investigated five lines of indigenous Korean native chicken (KNC) and the Ogye breed using next-generation sequencing (NGS) data with Geneious Prime-based assembly and variant calling with the Genome Analysis Toolkit (GATK) best practices pipeline. The consensus sequences of MHC-B (BG1-BF2) were obtained for each chicken line/breed and their variants were analyzed. All of the Korean native chicken lines possessed an excessive number of variants, including an ample amount of high-impact variants that provided useful information regarding modified major histocompatibility complex molecules. The study confirmed that next-generation sequencing techniques can effectively be used to detect MHC variabilities and the KNC lines are highly diverse for the MHC-B region, suggesting a substantial divergence from red junglefowl.
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Abstract
Compared to the major histocompatibility complex (MHC) of typical mammals, the chicken BF/BL region is small and simple, with most of the genes playing central roles in the adaptive immune response. However, some genes of the chicken MHC are almost certainly involved in innate immunity, such as the complement component C4 and the lectin-like receptor/ligand gene pair BNK and Blec. The poorly expressed classical class I molecule BF1 is known to be recognised by natural killer (NK) cells and, analogous to mammalian immune responses, the classical class I molecules BF1 and BF2, the CD1 homologs and the butyrophilin homologs called BG may be recognised by adaptive immune lymphocytes with semi-invariant receptors in a so-called adaptate manner. Moreover, the TRIM and BG regions next to the chicken MHC, along with the genetically unlinked Y and olfactory/scavenger receptor regions on the same chromosome, have multigene families almost certainly involved in innate and adaptate responses. On this chicken microchromosome, the simplicity of the adaptive immune gene systems contrasts with the complexity of the gene systems potentially involved in innate immunity.
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BTN2A2 protein negatively regulates T cells to ameliorate collagen-induced arthritis in mice. Sci Rep 2021; 11:19375. [PMID: 34588505 PMCID: PMC8481265 DOI: 10.1038/s41598-021-98443-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/06/2021] [Indexed: 12/05/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disorder characterized by persistent inflammatory responses in target tissues and organs, resulting in the destruction of joints. Collagen type II (CII)-induced arthritis (CIA) is the most used animal model for human RA. Although BTN2A2 protein has been previously shown to inhibit T cell functions in vitro, its effect on autoimmune arthritis has not been reported. In this study, we investigate the ability of a recombinant BTN2A2-IgG2a Fc (BTN2A2-Ig) fusion protein to treat CIA. We show here that administration of BTN2A2-Ig attenuates established CIA, as compared with control Ig protein treatment. This is associated with reduced activation, proliferation and Th1/Th17 cytokine production of T cells in BTN2A2-Ig-treated CIA mice. BTN2A2-Ig also inhibits CII-specific T cell proliferation and Th1/Th17 cytokine production. Although the percentage of effector T cells is decreased in BTN2A2-Ig-treated CIA mice, the proportions of naive T cells and regulatory T cells is increased. Furthermore, BTN2A2-Ig reduces the percentage of proinflammatory M1 macrophages but increases the percentage of anti-inflammatory M2 macrophages in the CIA mice. Our results suggest that BTN2A2-Ig protein has the potential to be used in the treatment of collagen-induced arthritis models.
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de Groot N, Groen R, Orie V, Bruijnesteijn J, de Groot NG, Doxiadis GGM, Bontrop RE. Analysis of macaque BTN3A genes and transcripts in the extended MHC: conserved orthologs of human γδ T cell modulators. Immunogenetics 2019; 71:545-559. [PMID: 31384962 PMCID: PMC6790196 DOI: 10.1007/s00251-019-01126-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022]
Abstract
Butyrophilins (BTN), specifically BTN3A, play a central role in the modulation of γδ T cells, which are mainly present in gut and mucosal tissues. BTN3A1 is known, for example, to activate Vγ9Vδ2 T cells by means of a phosphoantigen interaction. In the extended HLA region, three genes are located, designated BTN3A1, BTN3A2 and BTN3A3, which were also defined in rhesus macaques. In contrast to humans, rhesus monkeys have an additional gene, BTN3A3Like, which has the features of a pseudogene. cDNA analysis of 32 Indian rhesus and 16 cynomolgus macaques originating from multiple-generation families revealed that all three genes are oligomorphic, and the deduced amino acids display limited variation. The macaque BTN3A alleles segregated together with MHC alleles, proving their location in the extended (Major Histocompatibility Complex) MHC. BTN3A nearly full-length transcripts of macaques and humans cluster tightly together in the phylogenetic tree, suggesting that the genes represent true orthologs of each other. Despite the limited level of polymorphism, 15 Mamu- and 14 Mafa-BTN3A haplotypes were defined, and, as in humans, all three BTN3A genes are transcribed in PBMCs and colon tissues. In addition to regular full-length transcripts, a high number of various alternative splicing (AS) products were observed for all BTN3A alleles, which may result in different isoforms. The comparable function of certain subsets of γδ T cells in human and non-human primates in concert with high levels of sequence conservation observed for the BTN3A transcripts presents the opportunity to study these not yet well understood molecules in macaques as a model species.
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Affiliation(s)
- Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Rens Groen
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Vaneesha Orie
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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