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Vasoya D, Connelley T, Tzelos T, Todd H, Ballingall KT. Large scale transcriptional analysis of MHC class I haplotype diversity in sheep. HLA 2024; 103:e15356. [PMID: 38304958 DOI: 10.1111/tan.15356] [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: 10/25/2023] [Revised: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Domestic sheep (Ovis aries) have been an important component of livestock agricultural production for thousands of years. Preserving genetic diversity within livestock populations maintains a capacity to respond to changing environments and rapidly evolving pathogens. MHC genetic diversity can influence immune functionality at individual and population levels. Here, we focus on defining functional MHC class I haplotype diversity in a large cohort of Scottish Blackface sheep pre-selected for high levels of MHC class II DRB1 diversity. Using high-throughput amplicon sequencing with three independent sets of barcoded primers we identified 134 MHC class I transcripts within 38 haplotypes. Haplotypes were identified with between two and six MHC class I genes, plus variable numbers of conserved sequences with very low read frequencies. One or two highly transcribed transcripts dominate each haplotype indicative of two highly polymorphic, classical MHC class I genes. Additional clusters of medium, low, and very low expressed transcripts are described, indicative of lower transcribed classical, non-classical and genes whose function remains to be determined.
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Affiliation(s)
- Deepali Vasoya
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
| | - Timothy Connelley
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
| | - Thomas Tzelos
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
- Moredun Research Institute, Pentlands Science Park, Scotland, UK
| | - Helen Todd
- Moredun Research Institute, Pentlands Science Park, Scotland, UK
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Li TT, Xia T, Wu JQ, Hong H, Sun ZL, Wang M, Ding FR, Wang J, Jiang S, Li J, Pan J, Yang G, Feng JN, Dai YP, Zhang XM, Zhou T, Li T. De novo genome assembly depicts the immune genomic characteristics of cattle. Nat Commun 2023; 14:6601. [PMID: 37857610 PMCID: PMC10587341 DOI: 10.1038/s41467-023-42161-1] [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: 02/17/2023] [Accepted: 09/30/2023] [Indexed: 10/21/2023] Open
Abstract
Immunogenomic loci remain poorly understood because of their genetic complexity and size. Here, we report the de novo assembly of a cattle genome and provide a detailed annotation of the immunogenomic loci. The assembled genome contains 143 contigs (N50 ~ 74.0 Mb). In contrast to the current reference genome (ARS-UCD1.2), 156 gaps are closed and 467 scaffolds are located in our assembly. Importantly, the immunogenomic regions, including three immunoglobulin (IG) loci, four T-cell receptor (TR) loci, and the major histocompatibility complex (MHC) locus, are seamlessly assembled and precisely annotated. With the characterization of 258 IG genes and 657 TR genes distributed across seven genomic loci, we present a detailed depiction of immune gene diversity in cattle. Moreover, the MHC gene structures are integrally revealed with properly phased haplotypes. Together, our work describes a more complete cattle genome, and provides a comprehensive view of its complex immune-genome.
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Affiliation(s)
- Ting-Ting Li
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Tian Xia
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Jia-Qi Wu
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Hao Hong
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Zhao-Lin Sun
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Ming Wang
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan Xilu, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, No.2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Fang-Rong Ding
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Jing Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Shuai Jiang
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Jin Li
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Jie Pan
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
| | - Guang Yang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Jian-Nan Feng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Yun-Ping Dai
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No.2 Yuanmingyuan Xilu, Beijing, 100193, China
| | - Xue-Min Zhang
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China
- School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Tao Zhou
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China.
| | - Tao Li
- Nanhu Laboratory, National Center of Biomedical Analysis, Beijing, 100850, China.
- School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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Vasoya D, Tzelos T, Benedictus L, Karagianni AE, Pirie S, Marr C, Oddsdóttir C, Fintl C, Connelley T. High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure. Genes (Basel) 2023; 14:1422. [PMID: 37510326 PMCID: PMC10379315 DOI: 10.3390/genes14071422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The Major Histocompatibility Complex (MHC) genes play a key role in a number of biological processes, most notably in immunological responses. The MHCI and MHCII genes incorporate a complex set of highly polymorphic and polygenic series of genes, which, due to the technical limitations of previously available technologies, have only been partially characterized in non-model but economically important species such as the horse. The advent of high-throughput sequencing platforms has provided new opportunities to develop methods to generate high-resolution sequencing data on a large scale and apply them to the analysis of complex gene sets such as the MHC. In this study, we developed and applied a MiSeq-based approach for the combined analysis of the expressed MHCI and MHCII repertoires in cohorts of Thoroughbred, Icelandic, and Norwegian Fjord Horses. The approach enabled us to generate comprehensive MHCI/II data for all of the individuals (n = 168) included in the study, identifying 152 and 117 novel MHCI and MHCII sequences, respectively. There was limited overlap in MHCI and MHCII haplotypes between the Thoroughbred and the Icelandic/Norwegian Fjord horses, showcasing the variation in MHC repertoire between genetically divergent breeds, and it can be inferred that there is much more MHC diversity in the global horse population. This study provided novel insights into the structure of the expressed equine MHC repertoire and highlighted unique features of the MHC in horses.
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Affiliation(s)
- Deepali Vasoya
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Thomas Tzelos
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK
| | - Lindert Benedictus
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Anna Eleonora Karagianni
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Scott Pirie
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Celia Marr
- Rossdales Equine Hospital, Cotton End Road, Exning, Newmarket CD8 7NN, UK
| | - Charlotta Oddsdóttir
- The Institute for Experimental Pathology at Keldur, University of Iceland Keldnavegur 3, 112 Reykjavík, Iceland
| | - Constanze Fintl
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Timothy Connelley
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
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