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Plasil M, Futas J, Jelinek A, Burger PA, Horin P. Comparative Genomics of the Major Histocompatibility Complex (MHC) of Felids. Front Genet 2022; 13:829891. [PMID: 35309138 PMCID: PMC8924298 DOI: 10.3389/fgene.2022.829891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 02/15/2022] [Indexed: 12/25/2022] Open
Abstract
This review summarizes the current knowledge on the major histocompatibility complex (MHC) of the family Felidae. This family comprises an important domestic species, the cat, as well as a variety of free-living felids, including several endangered species. As such, the Felidae have the potential to be an informative model for studying different aspects of the biological functions of MHC genes, such as their role in disease mechanisms and adaptation to different environments, as well as the importance of genetic diversity for conservation issues in free-ranging or captive populations. Despite this potential, the current knowledge on the MHC in the family as a whole is fragmentary and based mostly on studies of the domestic cat and selected species of big cats. The overall structure of the domestic cat MHC is similar to other mammalian MHCs following the general scheme “centromere-MHC class I-MHC class III-MHC class II” with some differences in the gene contents. An unambiguously defined orthologue of the non-classical class I HLA-E gene has not been identified so far and the class II DQ and DP genes are missing or pseudogenized, respectively. A comparison with available genomes of other felids showed a generally high level of structural and sequence conservation of the MHC region. Very little and fragmentary information on in vitro and/or in vivo biological functions of felid MHC genes is available. So far, no association studies have indicated effects of MHC genetic diversity on a particular disease. No information is available on the role of MHC class I molecules in interactions with Natural Killer (NK) cell receptors or on the putative evolutionary interactions (co-evolution) of the underlying genes. A comparison of complex genomic regions encoding NK cell receptors (the Leukocyte Receptor Complex, LRC and the Natural Killer Cell Complex, NKC) in the available felid genomes showed a higher variability in the NKC compared to the LRC and the MHC regions. Studies of the genetic diversity of domestic cat populations and/or specific breeds have focused mainly on DRB genes. Not surprisingly, higher levels of MHC diversity were observed in stray cats compared to pure breeds, as evaluated by DRB sequencing as well as by MHC-linked microsatellite typing. Immunogenetic analysis in wild felids has only been performed on MHC class I and II loci in tigers, Namibian leopards and cheetahs. This information is important as part of current conservation tasks to assess the adaptive potential of endangered wild species at the human-wildlife interface, which will be essential for preserving biodiversity in a functional ecosystem.
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Affiliation(s)
- Martin Plasil
- Research Group Animal Immunogenomics, Ceitec Vetuni, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Jan Futas
- Research Group Animal Immunogenomics, Ceitec Vetuni, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - April Jelinek
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Pamela A. Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, VIA, Vienna, Austria
| | - Petr Horin
- Research Group Animal Immunogenomics, Ceitec Vetuni, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
- *Correspondence: Petr Horin,
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Ning Y, Roberts NJ, Qi J, Peng Z, Long Z, Zhou S, Gu J, Hou Z, Yang E, Ren Y, Lang J, Liang Z, Zhang M, Ma J, Jiang G. Inbreeding status and implications for Amur tigers. Anim Conserv 2021. [DOI: 10.1111/acv.12761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Y. Ning
- College of Life Science Jilin Agricultural University Changchun China
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - N. J. Roberts
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - J. Qi
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
- School of Forestry Northeast Forestry University Harbin China
| | - Z. Peng
- School of Basic Medical Sciences Nanchang University Nanchang China
| | - Z. Long
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - S. Zhou
- Heilongjiang Research Institute of Wildlife Harbin China
| | - J. Gu
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - Z. Hou
- College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - E. Yang
- Wildlife Conservation Society Hunchun China
| | - Y. Ren
- Wildlife Conservation Society Hunchun China
| | - J. Lang
- Jilin Hunchun Amur Tiger National Nature Reserve Hunchun China
| | - Z. Liang
- Heilongjiang Laoyeling Amur Tiger National Nature Reserve Dongning China
| | - M. Zhang
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - J. Ma
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - G. Jiang
- Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected Area Northeast Forestry University Harbin China
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Characterization of major histocompatibility complex class I, and class II DRB loci of captive and wild Indian leopards (Panthera pardus fusca). Genetica 2017; 145:541-558. [DOI: 10.1007/s10709-017-9979-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 08/14/2017] [Indexed: 10/19/2022]
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Saka T, Nishita Y, Masuda R. Low genetic variation in the MHC class II DRB gene and MHC-linked microsatellites in endangered island populations of the leopard cat (Prionailurus bengalensis) in Japan. Immunogenetics 2017; 70:115-124. [PMID: 28689276 DOI: 10.1007/s00251-017-1020-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/25/2017] [Indexed: 12/12/2022]
Abstract
Isolated populations of the leopard cat (Prionailurus bengalensis) on Tsushima and Iriomote islands in Japan are classified as subspecies P. b. euptilurus and P. b. iriomotensis, respectively. Because both populations have decreased to roughly 100, an understanding of their genetic diversity is essential for conservation. We genotyped MHC class II DRB exon 2 and MHC-linked microsatellite loci to evaluate the diversity of MHC genes in the Tsushima and Iriomote cat populations. We detected ten and four DRB alleles in these populations, respectively. A phylogenetic analysis showed DRB alleles from both populations to be closely related to those in other felid DRB lineages, indicating trans-species polymorphism. The MHC-linked microsatellites were more polymorphic in the Tsushima than in the Iriomote population. The MHC diversity of both leopard cat populations is much lower than in the domestic cat populations on these islands, probably due to inbreeding associated with founder effects, geographical isolation, or genetic drift. Our results predict low resistance of the two endangered populations to new pathogens introduced to the islands.
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Affiliation(s)
- Toshinori Saka
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, 060-0810, Japan
| | - Yoshinori Nishita
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, 060-0810, Japan.,Department of Biological Sciences, Faculty of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, 060-0810, Japan
| | - Ryuichi Masuda
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, 060-0810, Japan. .,Department of Biological Sciences, Faculty of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, 060-0810, Japan.
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Marmesat E, Schmidt K, Saveljev AP, Seryodkin IV, Godoy JA. Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus. BMC Evol Biol 2017; 17:158. [PMID: 28676046 PMCID: PMC5496644 DOI: 10.1186/s12862-017-1006-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/23/2017] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Demographic bottlenecks erode genetic diversity and may increase endangered species' extinction risk via decreased fitness and adaptive potential. The genetic status of species is generally assessed using neutral markers, whose dynamic can differ from that of functional variation due to selection. The MHC is a multigene family described as the most important genetic component of the mammalian immune system, with broad implications in ecology and evolution. The genus Lynx includes four species differing immensely in demographic history and population size, which provides a suitable model to study the genetic consequences of demographic declines: the Iberian lynx being an extremely bottlenecked species and the three remaining ones representing common and widely distributed species. We compared variation in the most variable exon of the MHCI and MHCII-DRB loci among the four species of the Lynx genus. RESULTS The Iberian lynx was characterised by lower number of MHC alleles than its sister species (the Eurasian lynx). However, it maintained most of the functional genetic variation at MHC loci present in the remaining and genetically healthier lynx species at all nucleotide, amino acid, and supertype levels. CONCLUSIONS Species-wide functional genetic diversity can be maintained even in the face of severe population bottlenecks, which caused devastating whole genome genetic erosion. This could be the consequence of divergent alleles being retained across paralogous loci, an outcome that, in the face of frequent gene conversion, may have been favoured by balancing selection.
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Affiliation(s)
- Elena Marmesat
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), C/Américo Vespucio, 26, 41092, Sevilla, Spain
| | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, 17-230, Białowieża, Poland
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, 79 Preobrazhenskaya Str, Kirov, 610000, Russia
| | - Ivan V Seryodkin
- Laboratory of Ecology and Conservation of Animals, Pacific Institute of Geography of Far East Branch of Russian Academy of Sciences, 7 Radio Street, Vladivostok, 690041, Russia
- Far Eastern Federal University, 8 Sukhanova Street, Vladivostok, 690091, Russia
| | - José A Godoy
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), C/Américo Vespucio, 26, 41092, Sevilla, Spain.
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Luo W, Wang X, Qu H, Qin G, Zhang H, Lin Q. Genomic structure and expression pattern of MHC IIα and IIβ genes reveal an unusual immune trait in lined seahorse Hippocampus erectus. FISH & SHELLFISH IMMUNOLOGY 2016; 58:521-529. [PMID: 27697560 DOI: 10.1016/j.fsi.2016.09.057] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/26/2016] [Accepted: 09/30/2016] [Indexed: 06/06/2023]
Abstract
The major histocompatibility complex (MHC) genes are crucial in the adaptive immune system, and the gene duplication of MHC in animals can generally result in immune flexibility. In this study, we found that the lined seahorse (Hippocampus erectus) has only one gene copy number (GCN) of MHC IIα and IIβ, which is different from that in other teleosts. Together with the lack of spleen and gut-associated lymphatic tissue (GALT), the seahorse may be referred to as having a partial but natural "immunodeficiency". Highly variable amino acid residues were found in the IIα and IIβ domains, especially in the α1 and β1 domains with 9.62% and 8.43% allelic variation, respectively. Site models revealed seven and ten positively selected positions in the α1 and β1 domains, respectively. Real-time PCR experiments showed high expression levels of the MHC II genes in intestine (In), gill (Gi) and trunk kidney (TK) and medium in muscle (Mu) and brood pouch (BP), and the expression levels were significantly up-regulated after bacterial infection. Specially, relative higher expression level of both MHC IIα and IIβ was found in Mu and BP when compared with other fish species, in which MHC II is expressed negligibly in Mu. These results indicate that apart from TK, Gi and In, MU and BP play an important role in the immune response against pathogens in the seahorse. In conclusion, high allelic variation and strong positive selection in PBR and relative higher expression in MU and BP are speculated to partly compensate for the immunodeficiency.
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Affiliation(s)
- Wei Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyue Qu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Huixian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
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Molecular polymorphism of MHC-DRB gene and genetic diversity analysis of captive forest musk deer (Moschus berezovskii). BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Lau Q, Igawa T, Komaki S, Satta Y. Characterisation of major histocompatibility complex class I genes in Japanese Ranidae frogs. Immunogenetics 2016; 68:797-806. [PMID: 27418258 PMCID: PMC5056945 DOI: 10.1007/s00251-016-0934-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/23/2016] [Indexed: 12/02/2022]
Abstract
The major histocompatibility complex (MHC) is a key component of adaptive immunity in all jawed vertebrates, and understanding the evolutionary mechanisms that have shaped these genes in amphibians, one of the earliest terrestrial tetrapods, is important. We characterised MHC class I variation in three common Japanese Rana species (Rana japonica, Rana ornativentris and Rana tagoi tagoi) and identified a total of 60 variants from 21 individuals. We also found evolutionary signatures of gene duplication, recombination and balancing selection (including trans-species polymorphism), all of which drive increased MHC diversity. A unique feature of MHC class I from these three Ranidae species includes low synonymous differences per site (dS) within species, which we attribute to a more recent diversification of these sequences or recent gene duplication. The resulting higher dN/dS ratio relative to other anurans studied could be related to stronger selection pressure at peptide binding sites. This is one of the first studies to investigate MHC in Japanese amphibians and permits further exploration of the polygenetic factors associated with resistance to infectious diseases.
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Affiliation(s)
- Quintin Lau
- Department of Evolutionary Studies of Biosystems, Sokendai (The Graduate University for Advanced Studies), Kamiyamaguchi 1560-35, Hayama, Kanagawa, 240-0193, Japan.
| | - Takeshi Igawa
- Global Career Design Center, Hiroshima University, 1-7-1, Higashi-Hiroshima, Hiroshima, 739-8514, Japan
| | - Shohei Komaki
- Division of Developmental Science, Graduate School for International Development and Cooperation, Hiroshima University, 1-5-1, Higashi-Hiroshima, Hiroshima, 739-8529, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, Sokendai (The Graduate University for Advanced Studies), Kamiyamaguchi 1560-35, Hayama, Kanagawa, 240-0193, Japan
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Yao YF, Dai QX, Li J, Ni QY, Zhang MW, Xu HL. Genetic diversity and differentiation of the rhesus macaque (Macaca mulatta) population in western Sichuan, China, based on the second exon of the major histocompatibility complex class II DQB (MhcMamu-DQB1) alleles. BMC Evol Biol 2014; 14:130. [PMID: 24930092 PMCID: PMC4070090 DOI: 10.1186/1471-2148-14-130] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 06/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rhesus macaques living in western Sichuan, China, have been separated into several isolated populations due to habitat fragmentation. Previous studies based on the neutral or nearly neutral markers (mitochondrial DNA or microsatellites) showed high levels of genetic diversity and moderate genetic differentiation in the Sichuan rhesus macaques. Variation at the major histocompatibility complex (MHC) loci is widely accepted as being maintained by balancing selection, even with a low level of neutral variability in some species. However, in small and isolated or bottlenecked populations, balancing selection may be overwhelmed by genetic drift. To estimate microevolutionary forces acting on the isolated rhesus macaque populations, we examined genetic variation at Mhc-DQB1 loci in 119 wild rhesus macaques from five geographically isolated populations in western Sichuan, China, and compared the levels of MHC variation and differentiation among populations with that previously observed at neutral microsatellite markers. RESULTS 23 Mamu-DQB1 alleles were identified in 119 rhesus macaques in western Sichuan, China. These macaques exhibited relatively high levels of genetic diversity at Mamu-DQB1. The Hanyuan population presented the highest genetic variation, whereas the Heishui population was the lowest. Analysis of molecular variance (AMOVA) and pairwise FST values showed moderate genetic differentiation occurring among the five populations at the Mhc-DQB1 locus. Non-synonymous substitutions occurred at a higher frequency than synonymous substitutions in the peptide binding region. Levels of MHC variation within rhesus macaque populations are concordant with microsatellite variation. On the phylogenetic tree for the rhesus and crab-eating macaques, extensive allele or allelic lineage sharing is observed between the two species. CONCLUSIONS Phylogenetic analyses confirm the apparent trans-species model of evolution of the Mhc-DQB1 genes in these macaques. Balancing selection plays an important role in sharing allelic lineages between species, but genetic drift may share balancing selection dominance to maintain MHC diversity. Great divergence at neutral or adaptive markers showed that moderate genetic differentiation had occurred in rhesus macaque populations in western Sichuan, China, due to the habitat fragmentation caused by long-term geographic barriers and human activity. The Heishui population should be paid more attention for its lowest level of genetic diversity and relatively great divergence from others.
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Affiliation(s)
- Yong-Fang Yao
- College of Animal Science and Technology, Sichuan Agricultural University, Ya´an 625014, China
| | - Qiu-Xia Dai
- College of Animal Science and Technology, Sichuan Agricultural University, Ya´an 625014, China
| | - Jing Li
- College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Qing-Yong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Ya´an 625014, China
| | - Ming-Wang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Ya´an 625014, China
| | - Huai-Liang Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Ya´an 625014, China
- Experimental Animal Engineering Center/National Experimental Macaque Reproduce Laboratory, Sichuan Agricultural Universiy, Ya′an 625014, China
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Holmes JC, Holmer SG, Ross P, Buntzman AS, Frelinger JA, Hess PR. Polymorphisms and tissue expression of the feline leukocyte antigen class I loci FLAI-E, FLAI-H, and FLAI-K. Immunogenetics 2013; 65:675-89. [PMID: 23812210 PMCID: PMC3777221 DOI: 10.1007/s00251-013-0711-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 05/18/2013] [Indexed: 01/14/2023]
Abstract
Cytotoxic CD8+ T-cell immunosurveillance for intracellular pathogens, such as viruses, is controlled by classical major histocompatibility complex (MHC) class Ia molecules, and ideally, these antiviral T-cell populations are defined by the specific peptide and restricting MHC allele. Surprisingly, despite the utility of the cat in modeling human viral immunity, little is known about the feline leukocyte antigen class I complex (FLAI). Only a few coding sequences with uncertain locus origin and expression patterns have been reported. Of 19 class I genes, three loci--FLAI-E, FLAI-H, and FLAI-K--are predicted to encode classical molecules, and our objective was to evaluate their status by analyzing polymorphisms and tissue expression. Using locus-specific, PCR-based genotyping, we amplified 33 FLAI-E, FLAI-H, and FLAI-K alleles from 12 cats of various breeds, identifying, for the first time, alleles across three distinct loci in a feline species. Alleles shared the expected polymorphic and invariant sites in the α1/α2 domains, and full-length cDNA clones possessed all characteristic class Ia exons. Alleles could be assigned to a specific locus with reasonable confidence, although there was evidence of potentially confounding interlocus recombination between FLAI-E and FLAI-K. Only FLAI-E, FLAI-H, and FLAI-K origin alleles were amplified from cDNAs of multiple tissue types. We also defined hypervariable regions across these genes, which permitted the assignment of names to both novel and established alleles. As predicted, FLAI-E, FLAI-H, and FLAI-K fulfill the major criteria of class Ia genes. These data represent a necessary prerequisite for studying epitope-specific antiviral CD8+ T-cell responses in cats.
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Affiliation(s)
- Jennifer C. Holmes
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Savannah G. Holmer
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Peter Ross
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Adam S. Buntzman
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Jeffrey A. Frelinger
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
| | - Paul R. Hess
- Immunology Program, and Department of Clinical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, United States of America
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Yao YF, Zhao JJ, Dai QX, Li JY, Zhou L, Wang YT, Ni QY, Zhang MW, Xu HL. Identification and characterization of the major histocompatibility complex class II DQB (MhcMath-DQB1) alleles in Tibetan macaques (Macaca thibetana). ACTA ACUST UNITED AC 2013; 82:113-21. [PMID: 23745600 DOI: 10.1111/tan.12145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/25/2013] [Accepted: 05/19/2013] [Indexed: 11/26/2022]
Abstract
Tibetan macaque (Macaca thibetana), an endangered primate species endemic to China, have been used as experimental animal model for various human diseases. Major histocompatibility complex (MHC) genes play a crucial role in the susceptibility and/or resistance to many human diseases, but little is known about Tibetan macaques. To gain an insight into the MHC background and to facilitate the experimental use of Tibetan macaques, the second exon of Mhc-DQB1 gene was sequenced in a cohort of wild Tibetan macaques living in the Sichuan province of China. A total of 23 MhcMath-DQB1 alleles were identified for the first time, illustrating a marked allelic polymorphism at the DQB1 locus for these macaques. Most of the sequences (74%) observed in this study belong to DQB1*06 (9 alleles) and DQB1*18 (8 alleles) lineages, and the rest (26%) belong to DQB1*15 (3 alleles) and DQB1*17 (3 alleles) lineages. The most frequent alleles detected among these macaques were MhcMath-DQB1*15:02:02 (17.9%), followed by Math-DQB1*06:06, 17:03 and 18:01, which were detected in 9 (16.1%) of the monkeys, respectively. Non-synonymous substitutions occurred at a significantly higher frequency than synonymous substitutions in the peptide-binding region, suggesting balancing selection for maintaining polymorphisms at the MHC class II DQB1 locus. Phylogenetic analyses confirms the trans-species model of evolution of the Mhc-DQB1 genes in non-human primates, and in particular, the extensive allele sharing is observed between Tibetan and other macaque species.
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Affiliation(s)
- Y-F Yao
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
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Weber DS, Van Coeverden De Groot PJ, Peacock E, Schrenzel MD, Perez DA, Thomas S, Shelton JM, Else CK, Darby LL, Acosta L, Harris C, Youngblood J, Boag P, Desalle R. Low MHC variation in the polar bear: implications in the face of Arctic warming? Anim Conserv 2013. [DOI: 10.1111/acv.12045] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- D. S. Weber
- Division of Natural Sciences; New College of Florida; Sarasota FL USA
- American Museum of Natural History; New York NY USA
| | | | - E. Peacock
- Department of Environment; The Government of Nunavut; Igloolik NU Canada
| | - M. D. Schrenzel
- San Diego Zoo Institute for Conservation Research; Escondido CA USA
| | - D. A. Perez
- American Museum of Natural History; New York NY USA
- Stevens Institute of Technology; Hoboken NJ USA
| | - S. Thomas
- San Diego Zoo Institute for Conservation Research; Escondido CA USA
| | - J. M. Shelton
- American Museum of Natural History; New York NY USA
- Brooklyn College; City University of New York; New York NY USA
| | | | - L. L. Darby
- American Museum of Natural History; New York NY USA
- Columbia University; New York NY USA
| | - L. Acosta
- American Museum of Natural History; New York NY USA
- Villanova University; Villanova PA USA
| | - C. Harris
- Biology Department; Queen's University; Kingston ON Canada
| | - J. Youngblood
- San Diego Zoo Institute for Conservation Research; Escondido CA USA
| | - P. Boag
- Biology Department; Queen's University; Kingston ON Canada
| | - R. Desalle
- American Museum of Natural History; New York NY USA
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Independent evolution of functional MHC class II DRB genes in New World bat species. Immunogenetics 2012; 64:535-47. [PMID: 22426641 DOI: 10.1007/s00251-012-0609-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 02/23/2012] [Indexed: 12/21/2022]
Abstract
Genes of the major histocompatibility complex (MHC) play a pivotal role in the vertebrate immune system and are attractive markers for functional, fitness-related, genetic variation. Although bats (Chiroptera) represent the second largest mammalian order and are prone to various emerging infectious diseases, little is known about MHC evolution in bats. In the present study, we examined expressed MHC class II DRB sequences (exons 1 to 4) of New World bat species, Saccopteryx bilineata, Carollia perspicillata, Noctilio albiventris and Noctilio leporinus (only exon 2). We found a wide range of copy number variation of DRB loci with one locus detected in the genus Noctilio and up to ten functional loci observed in S. bilineata. Sequence variation between alleles of the same taxa was high with evidence for positive selection. We found statistical support for recombination or gene conversion events among sequences within the same but not between bat species. Phylogenetic relationships among DRB alleles provided strong evidence for independent evolution of the functional MHC class II DRB genes in the three investigated species, either by recent gene duplication, or homogenization of duplicated loci by frequent gene conversion events. Phylogenetic analysis of all available chiropteran DRB exon 2 sequences confirmed their monophyletic origin within families, but revealed a possible trans-species mode of evolution pattern in congeneric bat species, e.g. within the genera Noctilio and Myotis. This is the first study investigating phylogenetic relationships of MHC genes within bats and therefore contributes to a better understanding of MHC evolution in one of the most dominant mammalian order.
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14
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Evidence for evolutionary convergence at MHC in two broadly distributed mesocarnivores. Immunogenetics 2011; 64:289-301. [DOI: 10.1007/s00251-011-0588-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 10/31/2011] [Indexed: 12/21/2022]
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15
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Castro-Prieto A, Wachter B, Melzheimer J, Thalwitzer S, Sommer S. Diversity and evolutionary patterns of immune genes in free-ranging Namibian leopards (Panthera pardus pardus). ACTA ACUST UNITED AC 2011; 102:653-65. [PMID: 21914667 DOI: 10.1093/jhered/esr097] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The genes of the major histocompatibility complex (MHC) are a key component of the mammalian immune system and have become important molecular markers for fitness-related genetic variation in wildlife populations. Currently, no information about the MHC sequence variation and constitution in African leopards exists. In this study, we isolated and characterized genetic variation at the adaptively most important region of MHC class I and MHC class II-DRB genes in 25 free-ranging African leopards from Namibia and investigated the mechanisms that generate and maintain MHC polymorphism in the species. Using single-stranded conformation polymorphism analysis and direct sequencing, we detected 6 MHC class I and 6 MHC class II-DRB sequences, which likely correspond to at least 3 MHC class I and 3 MHC class II-DRB loci. Amino acid sequence variation in both MHC classes was higher or similar in comparison to other reported felids. We found signatures of positive selection shaping the diversity of MHC class I and MHC class II-DRB loci during the evolutionary history of the species. A comparison of MHC class I and MHC class II-DRB sequences of the leopard to those of other felids revealed a trans-species mode of evolution. In addition, the evolutionary relationships of MHC class II-DRB sequences between African and Asian leopard subspecies are discussed.
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Affiliation(s)
- Aines Castro-Prieto
- Evolutionary Genetics, Research Groups at the Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, D-10315 Berlin, Germany
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16
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SCHMIDT K, RATKIEWICZ M, KONOPIŃSKI MK. The importance of genetic variability and population differentiation in the Eurasian lynx Lynx lynx for conservation, in the context of habitat and climate change. Mamm Rev 2011. [DOI: 10.1111/j.1365-2907.2010.00180.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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17
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MHC class I and MHC class II DRB gene variability in wild and captive Bengal tigers (Panthera tigris tigris). Immunogenetics 2010; 62:667-79. [PMID: 20821315 DOI: 10.1007/s00251-010-0475-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 08/26/2010] [Indexed: 10/19/2022]
Abstract
Bengal tigers are highly endangered and knowledge on adaptive genetic variation can be essential for efficient conservation and management. Here we present the first assessment of allelic variation in major histocompatibility complex (MHC) class I and MHC class II DRB genes for wild and captive tigers from India. We amplified, cloned, and sequenced alpha-1 and alpha-2 domain of MHC class I and beta-1 domain of MHC class II DRB genes in 16 tiger specimens of different geographic origin. We detected high variability in peptide-binding sites, presumably resulting from positive selection. Tigers exhibit a low number of MHC DRB alleles, similar to other endangered big cats. Our initial assessment-admittedly with limited geographic coverage and sample size-did not reveal significant differences between captive and wild tigers with regard to MHC variability. In addition, we successfully amplified MHC DRB alleles from scat samples. Our characterization of tiger MHC alleles forms a basis for further in-depth analyses of MHC variability in this illustrative threatened mammal.
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