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Minias P. Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers and life history. Mol Ecol 2024; 33:e17453. [PMID: 38953291 DOI: 10.1111/mec.17453] [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: 01/08/2024] [Revised: 06/05/2024] [Accepted: 06/14/2024] [Indexed: 07/03/2024]
Abstract
The major histocompatibility complex (MHC) multigene family encodes key pathogen-recognition molecules of the vertebrate adaptive immune system. Hyper-polymorphism of MHC genes is de novo generated by point mutations, but new haplotypes may also arise by re-shuffling of existing variation through intra- and inter-locus gene conversion. Although the occurrence of gene conversion at the MHC has been known for decades, we still have limited understanding of its functional importance. Here, I took advantage of extensive genetic resources (~9000 sequences) to investigate broad scale macroevolutionary patterns in gene conversion processes at the MHC across nearly 200 avian species. Gene conversion was found to constitute a universal mechanism in birds, as 83% of species showed footprints of gene conversion at either MHC class and 25% of all allelic variants were attributed to gene conversion. Gene conversion processes were stronger at MHC-II than MHC-I, but inter-specific variation at both MHC classes was explained by similar evolutionary scenarios, reflecting fluctuating selection towards different optima and drift. Gene conversion showed uneven phylogenetic distribution across birds and was driven by gene copy number variation, supporting significant role of inter-locus gene conversion processes in the evolution of the avian MHC. Finally, MHC gene conversion was stronger in species with fast life histories (high fecundity) and in long-distance migrants, likely reflecting variation in population sizes and host-pathogen coevolutionary dynamics. The results provide a robust comparative framework for understanding macroevolutionary variation in gene conversion at the avian MHC and reinforce important contribution of this mechanism to functional MHC diversity.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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2
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Zeng Q, Li X, Shi X, Yan S. Partial molecular characterization, expression pattern and polymorphism analysis of MHC I genes in Chinese domestic goose (Anser cygnoides). Genet Mol Biol 2024; 47:e20220252. [PMID: 39012094 PMCID: PMC11249561 DOI: 10.1590/1678-4685-gmb-2022-0252] [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: 10/06/2022] [Accepted: 05/09/2024] [Indexed: 07/17/2024] Open
Abstract
Major histocompatibility complex (MHC) allelic polymorphism is critically important for mediating antigen presentation in vertebrates. Presently, there are insufficient studies of MHC genetic diversity in domestic Anseriform birds. In this study, we analyzed the expression profile of MHC I genes and screened for MHC I exon 2 polymorphism in one domestic goose population from China using Illumina MiSeq sequencing. The results showed that four MHC I alleles (Ancy-IE2*09/*11/*13/*21) in one goose were identified based on cDNA cloning and sequencing using four primer combinations, and the varying number of cDNA clones implied that these four classical sequences showed differential expression patterns. Through next-generation sequencing, 27 alleles were obtained from 68 geese with 3-10 putative alleles per individual, indicating at least the existence of 5 MHC I loci in the goose. The marked excess of the non-synonymous over the synonymous substitution in the peptide-binding region (PBR) along 27 alleles and five positively selected sites (PSSs) detected around the PBR indicated that balancing selection might be the major force in shaping high MHC variation in the goose. Additionally, IA alleles displaying lower polymorphism were subject to less positive selection pressure than non-IA alleles with a higher level of polymorphism.
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Affiliation(s)
- Qianqian Zeng
- Qilu University of Technology, School of Bioengineering, State
Key Laboratory of Biobased Material and Green Papermaking, Jinan, Shandong,
China
| | - Xiaojie Li
- Qilu University of Technology, School of Bioengineering, State
Key Laboratory of Biobased Material and Green Papermaking, Jinan, Shandong,
China
| | - Xiaomin Shi
- Qilu University of Technology, School of Bioengineering, State
Key Laboratory of Biobased Material and Green Papermaking, Jinan, Shandong,
China
| | - Shigan Yan
- Qilu University of Technology, School of Bioengineering, State
Key Laboratory of Biobased Material and Green Papermaking, Jinan, Shandong,
China
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3
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Youk S, Kang M, Ahn B, Koo Y, Park C. Genetic Diversity and Sequence Conservation of Peptide-Binding Regions of MHC Class I Genes in Pig, Cattle, Chimpanzee, and Human. Genes (Basel) 2023; 15:7. [PMID: 38275589 PMCID: PMC10815642 DOI: 10.3390/genes15010007] [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: 11/30/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Comparative analyses of MHC gene diversity and evolution across different species could offer valuable insights into the evolution of MHC genes. Intra- and inter-species sequence diversity and conservation of 12 classical major histocompatibility complex (MHC) class I genes from cattle, chimpanzees, pigs, and humans was analyzed using 20 representative allelic groups for each gene. The combined analysis of paralogous loci for each species revealed that intra-locus amino-acid sequence variations in the peptide-binding region (PBR) of MHC I genes did not differ significantly between species, ranging from 8.44% for SLA to 10.75% for BoLA class I genes. In contrast, intraspecies differences in the non-PBRs of these paralogous genes were more pronounced, varying from 4.59% for SLA to 16.89% for HLA. Interestingly, the Shannon diversity index and rate of nonsynonymous substitutions for PBR were significantly higher in SLA and BoLA than those in Patr and HLA. Analysis of peptide-binding pockets across all analyzed MHC class I genes of the four species indicated that pockets A and E showed the lowest and highest diversity, respectively. The estimated divergence times suggest that primate and artiodactyl MHC class I genes diverged 60.41 Mya, and BoLA and SLA genes diverged 35.34 Mya. These results offer new insights into the conservation and diversity of MHC class I genes in various mammalian species.
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Affiliation(s)
- Seungyeon Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| | - Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
| | - Yangmo Koo
- Genetic & Breeding Department, Korea Animal Improvement Association, Seocho, Seoul 06668, Republic of Korea;
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul 05029, Republic of Korea; (S.Y.); (M.K.); (B.A.)
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Xu N, Ye W, Sun C, He K, Zhu Y, Lan H, Lu C, Liu H. Genetic Diversity and Differentiation of MHC Class I Genes in Red-Crowned Crane Populations. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.898581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The red-crowned crane (Grus japonensis) has been demoted to “vulnerable species” because its populations have apparently stabilized in Japan and Korea. Low variation and genetic drift may cause damage to the nascent recovery of the G. japonensis population. The major histocompatibility complex (MHC) is one of the most polymorphic gene families in the vertebrate genome and can reflect information on the adaptive evolution of endangered species. In this study, variations in MHC I exon 3 of captive G. japonensis in China were assessed and compared with those in cranes from Japan. Forty MHC alleles of 274 base pairs were isolated from 32 individuals from two captive populations in China. There was high variability in the nucleotide and amino acid composition, showing the proportion of polymorphic sites of 18.98 and 32.97%, respectively. Comparative analyses of the Chinese and Japanese populations based on 222 base pair sequences revealed more alleles and higher variation in the Chinese population. The lack of significant geographical differentiation of G. japonensis was supported by the genetic differentiation coefficient (0.04506) between the Chinese and Japanese populations. Positive selection of antigen-binding sites was observed, which contributed to maintaining the diversity of MHC class I genes. Phylogenetic analysis suggested the persistence of trans-species polymorphisms among MHC class I genes in Gruidae species. Our results may contribute to optimizing the management of G. japonensis populations and population recovery of this threatened species.
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He K, Liang CH, Zhu Y, Dunn P, Zhao A, Minias P. Reconstructing Macroevolutionary Patterns in Avian MHC Architecture With Genomic Data. Front Genet 2022; 13:823686. [PMID: 35251132 PMCID: PMC8893315 DOI: 10.3389/fgene.2022.823686] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/25/2022] [Indexed: 12/28/2022] Open
Abstract
The Major Histocompatibility Complex (MHC) is a hyper-polymorphic genomic region, which forms a part of the vertebrate adaptive immune system and is crucial for intra- and extra-cellular pathogen recognition (MHC-I and MHC-IIA/B, respectively). Although recent advancements in high-throughput sequencing methods sparked research on the MHC in non-model species, the evolutionary history of MHC gene structure is still poorly understood in birds. Here, to explore macroevolutionary patterns in the avian MHC architecture, we retrieved contigs with antigen-presenting MHC and MHC-related genes from available genomes based on third-generation sequencing. We identified: 1) an ancestral avian MHC architecture with compact size and tight linkage between MHC-I, MHC-IIA/IIB and MHC-related genes; 2) three major patterns of MHC-IIA/IIB unit organization in different avian lineages; and 3) lineage-specific gene translocation events (e.g., separation of the antigen-processing TAP genes from the MHC-I region in passerines), and 4) the presence of a single MHC-IIA gene copy in most taxa, showing evidence of strong purifying selection (low dN/dS ratio and low number of positively selected sites). Our study reveals long-term macroevolutionary patterns in the avian MHC architecture and provides the first evidence of important transitions in the genomic arrangement of the MHC region over the last 100 million years of bird evolution.
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Affiliation(s)
- Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
- *Correspondence: Ke He, ; Piotr Minias,
| | - Chun-hong Liang
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Ying Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Peter Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Ayong Zhao
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Hangzhou, China
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łodz, Łódź, Poland
- *Correspondence: Ke He, ; Piotr Minias,
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Qin S, Dunn PO, Yang Y, Liu H, He K. Polymorphism and varying selection within the MHC class I of four Anas species. Immunogenetics 2021; 73:395-404. [PMID: 34195858 DOI: 10.1007/s00251-021-01222-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/23/2021] [Indexed: 10/21/2022]
Abstract
Ducks (Anatidae) are often vectors for the spread of pathogens because of their long-distance migrations. These migrations also expose ducks to a wide variety of pathogens in their wintering and breeding grounds, and, as a consequence, we might expect strong selection on their immune genes. Here, we studied exons 2 and 3 of the MHC class I in four species of Anas ducks (A. platyrhynchos, A. poecilorhyncha, A. formosa, and A. querquedula) using Illumina-sequencing. Both exons 2 and 3 code for the peptide-binding region of class I molecules; however, most previous studies of birds have only focused on exon 3. Here, we found stronger positive selection on exon 2 than exon 3, as indicated by more species with dN/dS > 1 and higher Wu-Kabat values. There was little evidence that divergence time influenced polymorphism, the numbers of identical alleles (partial α1 or α2 regions) among four Anas, or selection, suggesting that these widespread species might share similar levels of selection from pathogens. The high similarity of allele numbers, positively selected sites (PSS), conserved motifs, and variable protein sites (VPS) supported the persistence of trans-species polymorphism in Anas for at least 10 million years. Our study revealed exon 2 as a relatively unexplored source of variation in avian MHC class I, which should be considered in future studies.
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Affiliation(s)
- Shidi Qin
- College of Animal Science and Technology, College of Veterinary Medicine, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Agriculture and Forestry University, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, Hangzhou, China
| | - Peter O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, USA
| | - Yang Yang
- College of Animal Science and Technology, College of Veterinary Medicine, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Agriculture and Forestry University, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, Hangzhou, China
| | - Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Agriculture and Forestry University, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, Hangzhou, China.
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Minias P, He K, Dunn PO. The strength of selection is consistent across both domains of the MHC class I peptide-binding groove in birds. BMC Ecol Evol 2021; 21:80. [PMID: 33964878 PMCID: PMC8106206 DOI: 10.1186/s12862-021-01812-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/28/2021] [Indexed: 02/26/2023] Open
Abstract
Background The Major Histocompatibility Complex (MHC) codes for the key vertebrate immune receptors responsible for pathogen recognition. Foreign antigens are recognized via their compatibility to hyper-variable region of the peptide-binding groove (PBR), which consists of two separate protein domains. Specifically, the PBR of the MHC class I receptors, which recognize intra-cellular pathogens, has two α domains encoded by exon 2 (α1) and exon 3 (α2) of the same gene. Most research on avian MHC class I polymorphism has traditionally focused exclusively on exon 3 and comparisons of selection between the two domains have been hampered by the scarcity of molecular data for exon 2. Thus, it is not clear whether the two domains vary in their specificity towards different antigens and whether they are subject to different selective pressure. Results Here, we took advantage of rapidly accumulating genomic resources to test for the differences in selection patterns between both MHC class I domains of the peptide-binding groove in birds. For this purpose, we compiled a dataset of MHC class I exon 2 and 3 sequences for 120 avian species from 46 families. Our phylogenetically-robust approach provided strong evidence for highly consistent levels of selection on the α1 and α2 domains. There were strong correlations in all selection measures (number of positively/negatively selected residues and dN/dS ratios) between both PBR exons. Similar positive associations were found for the level of amino acid polymorphism across the two domains. Conclusions We conclude that the strength of selection and the level of polymorphism are highly consistent between both peptide-binding domains (α1 and α2) of the avian MHC class I. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01812-x.
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Affiliation(s)
- Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90-237, Łódź, Poland.
| | - Ke He
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Peter O Dunn
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, USA
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Ghani MU, Bo L, Buyang A, Yanchun X, Hussain S, Yasir M. Molecular Characterization of MHC Class I Genes in Four Species of the Turdidae Family to Assess Genetic Diversity and Selection. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5585687. [PMID: 33937397 PMCID: PMC8055405 DOI: 10.1155/2021/5585687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022]
Abstract
In vertebrate animals, the molecules encoded by major histocompatibility complex (MHC) genes play an essential role in the adaptive immunity. MHC class I deals with intracellular pathogens (virus) in birds. MHC class I diversity depends on the consequence of local and global environment selective pressure and gene flow. Here, we evaluated the MHC class I gene in four species of the Turdidae family from a broad geographical area of northeast China. We isolated 77 MHC class I sequences, including 47 putatively functional sequences and 30 pseudosequences from 80 individuals. Using the method based on analysis of cloned amplicons (n = 25) for each species, we found two and seven MHC I sequences per individual indicating more than one MHC I locus identified in all sampled species. Results revealed an overall elevated genetic diversity at MHC class I, evidence of different selection patterns among the domains of PBR and non-PBR. Alleles are found to be divergent with overall polymorphic sites per species ranging between 58 and 70 (out of 291 sites). Moreover, transspecies alleles were evident due to convergent evolution or recent speciation for the genus. Phylogenetic relationships among MHC I show an intermingling of alleles clustering among the Turdidae family rather than between other passerines. Pronounced MHC I gene diversity is essential for the existence of species. Our study signifies a valuable tool for the characterization of evolutionary relevant difference across a population of birds with high conservational concerns.
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Affiliation(s)
- Muhammad Usman Ghani
- College of Wildlife Resources and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Li Bo
- College of Wildlife Resources and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - An Buyang
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Science, Kyushu University, Fukuoka 810-0000, Japan
| | - Xu Yanchun
- College of Wildlife Resources and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Shakeel Hussain
- College of Wildlife Resources and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Muhammad Yasir
- Department of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Liu HY, He K, Ge YF, Wan QH, Fang SG. Cape Feather Coloration Signals Different Genotypes of the Most Polymorphic MHC Locus in Male Golden Pheasants ( Chrysolophus pictus). Animals (Basel) 2021; 11:ani11020276. [PMID: 33499157 PMCID: PMC7912351 DOI: 10.3390/ani11020276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
Ornamental feather coloration is usually a reflection of male quality and plays an important role during courtship, whereas the essence of male quality at the genetic level is not well understood. Major histocompatibility complex (MHC)-based mate choice has been observed in various vertebrates. Here, we investigated the relationship between the coloration of cape feathers and the MHC genotypes in golden pheasants (Chrysolophus pictus). We found that feather coloration differed sharply among different individuals (brightness: 1827.20 ± 759.43, chroma: 1241.90 ± 468.21, hue: 0.46 ± 0.06). Heterozygous individuals at the most polymorphic MHC locus (IA2) had brighter feathers than homozygous individuals (Z = -2.853, p = 0.004) and were more saturated in color (Z = -2.853, p = 0.004). However, feather coloration was not related to other MHC loci or to overall genetic heterozygosity (p > 0.050). Our study suggested that coloration of cape feathers might signal IA2 genotypes in golden pheasants.
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Affiliation(s)
- Hong-Yi Liu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.-Y.L.); (K.H.); (Y.-F.G.); (Q.-H.W.)
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Ke He
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.-Y.L.); (K.H.); (Y.-F.G.); (Q.-H.W.)
| | - Yun-Fa Ge
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.-Y.L.); (K.H.); (Y.-F.G.); (Q.-H.W.)
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.-Y.L.); (K.H.); (Y.-F.G.); (Q.-H.W.)
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.-Y.L.); (K.H.); (Y.-F.G.); (Q.-H.W.)
- Correspondence:
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10
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Zhao B, Zhang X, Li B, Du P, Shi L, Dong Y, Gao X, Sha W, Zhang H. Evolution of major histocompatibility complex class I genes in the sable Martes zibellina (Carnivora, Mustelidae). Ecol Evol 2020; 10:3439-3449. [PMID: 32274000 PMCID: PMC7141072 DOI: 10.1002/ece3.6140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/31/2020] [Accepted: 02/04/2020] [Indexed: 11/10/2022] Open
Abstract
The molecules encoded by major histocompatibility complex (MHC) genes play an essential role in the adaptive immune response among vertebrates. We investigated the molecular evolution of MHC class I genes in the sable Martes zibellina. We isolated 26 MHC class I sequences, including 12 putatively functional sequences and 14 pseudogene sequences, from 24 individuals from two geographic areas of northeast China. The number of putatively functional sequences found in a single individual ranged from one to five, which might be at least 1-3 loci. We found that both balancing selection and recombination contribute to evolution of MHC class I genes in M. zibellina. In addition, we identified a candidate nonclassical MHC class I lineage in Carnivora, which may have preceded the divergence (about 52-57 Mya) of Caniformia and Feliformia. This may contribute to further understanding of the origin and evolution of nonclassical MHC class I genes. Our study provides important immune information of MHC for M. zibellina, as well as other carnivores.
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Affiliation(s)
- Baojun Zhao
- College of Life Science Qufu Normal University Qufu China
| | - Xue Zhang
- College of Life Science Qufu Normal University Qufu China
| | - Bo Li
- College of Wildlife and Protected Area Northeast Forestry University Harbin China
| | - Pengfei Du
- College of Life Science Qufu Normal University Qufu China
| | - Lupeng Shi
- College of Life Science Qufu Normal University Qufu China
| | - Yuehuan Dong
- College of Life Science Qufu Normal University Qufu China
| | - Xiaodong Gao
- College of Life Science Qufu Normal University Qufu China
| | - Weilai Sha
- College of Life Science Qufu Normal University Qufu China
| | - Honghai Zhang
- College of Life Science Qufu Normal University Qufu China
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Pardal S, Drews A, Alves JA, Ramos JA, Westerdahl H. Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit. Immunogenetics 2017; 69:463-478. [PMID: 28534224 PMCID: PMC5486808 DOI: 10.1007/s00251-017-0993-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/22/2017] [Indexed: 11/29/2022]
Abstract
The major histocompatibility complex (MHC) encodes proteins that are central for antigen presentation and pathogen elimination. MHC class I (MHC-I) genes have attracted a great deal of interest among researchers in ecology and evolution and have been partly characterized in a wide range of bird species. So far, the main focus has been on species within the bird orders Galliformes and Passeriformes, while Charadriiformes remain vastly underrepresented with only two species studied to date. These two Charadriiformes species exhibit striking differences in MHC-I characteristics and MHC-I diversity. We therefore set out to study a third species within Charadriiformes, the Icelandic subspecies of black-tailed godwits (Limosa limosa islandica). This subspecies is normally confined to parasite-poor environments, and we hence expected low MHC diversity. MHC-I was partially characterized first using Sanger sequencing and then using high-throughput sequencing (MiSeq) in 84 individuals. We verified 47 nucleotide alleles in open reading frame with classical MHC-I characteristics, and each individual godwit had two to seven putatively classical MHC alleles. However, in contrast to previous MHC-I data within Charadriiformes, we did not find any evidence of alleles with low sequence diversity, believed to represent non-classical MHC genes. The diversity and divergence of the godwits MHC-I genes to a large extent fell between the previous estimates within Charadriiformes. However, the MHC genes of the migratory godwits had few sites subject to positive selection, and one possible explanation could be a low exposure to pathogens.
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Affiliation(s)
- Sara Pardal
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal.
| | - Anna Drews
- MEEL - Molecular Ecology and Evolution Laboratory, Lund University, Ecology building, SE-223 62, Lund, Sweden.
| | - José A Alves
- CESAM - Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.,South Iceland Research Centre, University of Iceland, Fjolheimer, IS-800, Selfoss, Iceland
| | - Jaime A Ramos
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Helena Westerdahl
- MEEL - Molecular Ecology and Evolution Laboratory, Lund University, Ecology building, SE-223 62, Lund, Sweden
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12
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Historical gene flow and profound spatial genetic structure among golden pheasant populations suggested by multi-locus analysis. Mol Phylogenet Evol 2017; 110:93-103. [PMID: 28286102 DOI: 10.1016/j.ympev.2017.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 12/06/2016] [Accepted: 03/06/2017] [Indexed: 12/23/2022]
Abstract
Major histocompatibility complex (MHC) is a good marker system for geographical genetics since they are functional genes in the immune system that are likely to affect the fitness of the individual, and the survival and evolutionary potential of a population in a changing environment. Golden pheasant (Chrysolophus pictus) is a wild Phasianidae distributed in central and north China. In this study, we used a locus-specific genotyping technique for MHC IIB genes of golden pheasant. Combining with microsatellites (simple sequence repeat, SSR) and mitochondrial DNA (mtDNA) D-loop region, we investigated the demographic history and illuminate genetic structure of this bird in detail. SYR (south of Yangtze river) - NYR (north of Yangtze river) lineages, separated by Yangtze River, were defined in genetic structure of MHC IIB. NYR was supposed as refuge during glacial period, suggested by diversity parameters and more ancient alleles in this region. Based on this hypothesis, there was gene flow from NYR to SYR, which was proved by three pieces of evidence: (1) distinct demographic histories of SYR (kept stable) and NYR (experienced expansion); (2) specific affiliation of LC in genetic structure of SSR and MHC genes; (3) significant gene flow from NYR to SYR. Moreover, we also found balancing selection by combination of three Grouping A2's regions (SC, QL and North) into one in Grouping B4 (NYR) and no pattern of isolation by distance (IBD) found in MHC IIB, whereas for SSR we found a relatively strong and significant IBD. Several mechanisms in the evolution of MHC IIB genes, including recombination, historically positive selection, trans-species evolution and concerted evolution, were shown by molecular and phylogenetic analysis. Overall these results suggest the Yangtze River was inferred to be a geological barrier for this avian and NYR might experience population expansion, which invaded into a neighboring region. This study contributes to the understanding of the effects of geographic features on contemporary patterns of genetic variation in the golden pheasant in China, and helps us to define the adaptive unite (AU) for this avian.
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