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Heimeier D, Garland EC, Eichenberger F, Garrigue C, Vella A, Baker CS, Carroll EL. A pan-cetacean MHC amplicon sequencing panel developed and evaluated in combination with genome assemblies. Mol Ecol Resour 2024; 24:e13955. [PMID: 38520161 DOI: 10.1111/1755-0998.13955] [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: 05/19/2023] [Revised: 12/01/2023] [Accepted: 12/22/2023] [Indexed: 03/25/2024]
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non-model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast-evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full-length gene sequences to design pan-cetacean primers that amplified the complete exon 2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy-number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno-Polymorphism Database (IPD-MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.
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Affiliation(s)
- Dorothea Heimeier
- School of Biological Sciences, University of Auckland-Waipapa Taumata Rau, Auckland, New Zealand
| | - Ellen C Garland
- Sea Mammal Research Unit, School of Biology, University of St. Andrews, Fife, UK
| | - Franca Eichenberger
- Sea Mammal Research Unit, School of Biology, University of St. Andrews, Fife, UK
| | - Claire Garrigue
- UMR ENTROPIE, (IRD, Université de La Réunion, Université de la Nouvelle-Calédonie, IFREMER, CNRS, Laboratoire d'Excellence-CORAIL), Nouméa, New Caledonia
- Opération Cétacés, Nouméa, New Caledonia
| | - Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida, Malta
| | - C Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Corvallis, Oregon, USA
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland-Waipapa Taumata Rau, Auckland, New Zealand
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Day G, Robb K, Oxley A, Telonis-Scott M, Ujvari B. Organisation and evolution of the major histocompatibility complex class I genes in cetaceans. iScience 2024; 27:109590. [PMID: 38632986 PMCID: PMC11022044 DOI: 10.1016/j.isci.2024.109590] [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: 04/26/2023] [Revised: 09/30/2023] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
A quarter of marine mammals are at risk of extinction, with disease and poor habitat quality contributing to population decline. Investigation of the Major Histocompatibility Complex (MHC) provides insight into species' capacity to respond to immune and environmental challenges. The eighteen available cetacean chromosome level genomes were used to annotate MHC Class I loci, and to reconstruct the phylogenetic relationship of the described loci. The highest number of loci was observed in the striped dolphin (Stenella coeruleoalba), while the least was observed in the pygmy sperm whale (Kogia breviceps) and rough toothed dolphin (Steno bredanensis). Of the species studied, Mysticetes had the most pseudogenes. Evolutionarily, MHC Class I diverged before the speciation of cetaceans. Yet, locus one was genomically and phylogenetically similar in many species, persisting over evolutionary time. This characterisation of MHC Class I in cetaceans lays the groundwork for future population genetics and MHC expression studies.
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Affiliation(s)
- Grace Day
- School of Life and Environmental Sciences, Deakin University, Geelong 3216, VIC, Australia
- Marine Mammal Foundation, Melbourne 3194, VIC, Australia
| | - Kate Robb
- Marine Mammal Foundation, Melbourne 3194, VIC, Australia
| | - Andrew Oxley
- School of Life and Environmental Sciences, Deakin University, Geelong 3216, VIC, Australia
| | - Marina Telonis-Scott
- School of Life and Environmental Sciences, Deakin University, Melbourne 3125, VIC, Australia
| | - Beata Ujvari
- School of Life and Environmental Sciences, Deakin University, Geelong 3216, VIC, Australia
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Arbanasić H, Medrano-González L, Hrenar T, Mikelić A, Gomerčić T, Svetličić I, Pavlinec Ž, Đuras M, Galov A. Recent selection created distinctive variability patterns on MHC class II loci in three dolphin species from the Mediterranean Sea. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 150:105079. [PMID: 37832898 DOI: 10.1016/j.dci.2023.105079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/15/2023]
Abstract
The major histocompatibility complex (MHC) includes highly polymorphic genes involved in antigen presentation, which is crucial for adaptive immune response. They represent fitness related genetic markers particularly informative for populations exposed to environmental challenges. Here we analyse the diversity and evolutionary traits of MHC class II DQA and DQB genes in the dolphins Stenella coeruleoalba and Grampus griseus from the Mediterranean Sea. We found substantial nucleotide and functional diversity, as well as strong evidence of balancing selection indicated by allele and supertype frequencies, Tajima's D statistics and dN/dS tests. The Risso's dolphin, considered the least abundant in the region, showed the effect of divergent allele advantage at the nucleotide and functional-peptide levels. An outstanding polymorphism was found in the striped dolphin, particularly intriguing in the DQA gene where the Ewens-Watterson test detected a selection sweep that occurred in recent history. We hypothesize that morbillivirus, which has recurrently invaded Mediterranean populations over the last decades, exerted the detected selective pressure.
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Affiliation(s)
- Haidi Arbanasić
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
| | - Luis Medrano-González
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.
| | - Tomica Hrenar
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
| | - Ana Mikelić
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
| | - Tomislav Gomerčić
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia.
| | - Ida Svetličić
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
| | - Željko Pavlinec
- Croatian Academy of Sciences and Arts, Trg Nikole Šubića Zrinskog 11, 10000, Zagreb, Croatia.
| | - Martina Đuras
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia.
| | - Ana Galov
- Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia.
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Characterization of two MHC II genes (DOB, DRB) in white-tailed deer (Odocoileus virginianus). BMC Genet 2020; 21:83. [PMID: 32727360 PMCID: PMC7392685 DOI: 10.1186/s12863-020-00889-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/16/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) is responsible for detecting and addressing foreign pathogens inside the body. While the general structure of MHC genes is relatively well conserved among mammalian species, it is notably different among ruminants due to a chromosomal inversion that splits MHC type II genes into two subregions (IIa, IIb). Recombination rates are reportedly high between these subregions, and a lack of linkage has been documented in domestic ruminants. However, no study has yet examined the degree of linkage between these subregions in a wild ruminant. The white-tailed deer (Odocoileus virginianus), a popular ruminant of the Cervidae family, is habitually plagued by pathogens in its natural environment (e.g. Haemonchus contortus, Elaeophora). Due to the association between MHC haplotypes and disease susceptibility, a deeper understanding of MHC polymorphism and linkage between MHC genes can further aid in this species' successful management. We sequenced MHC-DRB exon 2 (IIa) and MHC-DOB exon 2 (IIb) on the MiSeq platform from an enclosed white-tailed deer population located in Alabama. RESULTS We identified 12 new MHC-DRB alleles, and resampled 7 alleles, which along with other published alleles brings the total number of documented alleles in white-tailed deer to 30 for MHC-DRB exon 2. The first examination of MHC-DOB in white-tailed deer found significantly less polymorphism (11 alleles), as was expected of a non-classical MHC gene. While MHC-DRB was found to be under positive, diversifying selection, MHC-DOB was found to be under purifying selection for white-tailed deer. We found no significant linkage disequilibrium between MHC-DRB and MHC-DOB, suggesting that these loci are unlikely to be closely linked. CONCLUSIONS Overall, this study identified 12 new MHC-DRB exon 2 alleles and characterized a new, non-classical, MHC II gene (MHC-DOB) for white-tailed deer. We also found a lack of significant linkage between these two loci, which supports previous findings of a chromosomal inversion within the MHC type II gene region in ruminants, and suggests that white-tailed deer may have a recombination hotspot between these MHC regions similar to that found for Bos taurus.
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Tian R, Seim I, Zhang Z, Yang Y, Ren W, Xu S, Yang G. Distinct evolution of toll-like receptor signaling pathway genes in cetaceans. Genes Genomics 2019; 41:1417-1430. [PMID: 31535317 DOI: 10.1007/s13258-019-00861-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The relatively rapid spread and diversity of marine pathogens posed an initial and ongoing challenge for cetaceans (whales, dolphins, and porpoises), descendants of terrestrial mammals that transitioned from land to sea approximately 56 million years ago. Toll-like receptors (TLRs) play important roles in regulating immunity against pathogen infections by detecting specific molecular patterns and activating a wide range of downstream signaling pathways. The ever-increasing catalogue of mammalian genomes offers unprecedented opportunities to reveal genetic changes associated with evolutionary and ecological processes. OBJECTIVE This study aimed to explore the molecular evolution of TLR signaling pathway genes in cetaceans. METHODS Genes involved in the TLR signaling pathway were retrieved by BLAST searches using human coding sequences as queries. We tested each gene for positive selection along the cetacean branches using PAML and Hyphy. Physicochemical property changes of amino acids at all positively selected residues were assessed by TreeSAAP and visualized with WebLogo. Bovine and dolphin TLR4 was assessed using human embryonic kidney cell line HEK293, which lacks TLR4 and its co-receptor MD-2. RESULTS We demonstrate that eight TLR signaling pathway genes are under positive selection in cetaceans. These include key genes in the response to Gram-negative bacteria: TLR4, CD14, and LY96 (MD-2). Moreover, 41 out of 65 positively selected sites were inferred to harbor substitution that dramatically changes the physicochemical properties of amino acids, with most of them situated in or adjacent to functional regions. We also found strong evidence that positive selection occurred in the lineage of the Yangtze finless porpoise, likely reflecting relatively recent adaptions to a freshwater milieu. Species-specific differences in TLR4 response were observed between cetacean and terrestrial species. Cetacean TLR4 was significantly less responsive to lipopolysaccharides from a terrestrial E. coli strain, possibly a reflection of the arms race of host-pathogen co-evolution faced by cetaceans in an aquatic environment. CONCLUSION This study provides further impetus for studies on the evolution and function of the cetacean immune system.
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Affiliation(s)
- Ran Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.,Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.,Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Zepeng Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Ying Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
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