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Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals. Sci Rep 2022; 12:17933. [PMID: 36289307 PMCID: PMC9606363 DOI: 10.1038/s41598-022-21658-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/29/2022] [Indexed: 01/20/2023] Open
Abstract
The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother-offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.
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Shen T, He X, Lei M, Wang J, Li X, Li J. Cloning and structure of a histocompatibility class IIA gene (Lelo-DAA) in Chinese longsnout catfish (Leiocassis longirostris). Genes Genomics 2014. [DOI: 10.1007/s13258-014-0208-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Osborne AJ, Zavodna M, Chilvers BL, Robertson BC, Negro SS, Kennedy MA, Gemmell NJ. Extensive variation at MHC DRB in the New Zealand sea lion (Phocarctos hookeri) provides evidence for balancing selection. Heredity (Edinb) 2013; 111:44-56. [PMID: 23572124 PMCID: PMC3692317 DOI: 10.1038/hdy.2013.18] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Revised: 12/20/2012] [Accepted: 01/28/2013] [Indexed: 11/09/2022] Open
Abstract
Marine mammals are often reported to possess reduced variation of major histocompatibility complex (MHC) genes compared with their terrestrial counterparts. We evaluated diversity at two MHC class II B genes, DQB and DRB, in the New Zealand sea lion (Phocarctos hookeri, NZSL) a species that has suffered high mortality owing to bacterial epizootics, using Sanger sequencing and haplotype reconstruction, together with next-generation sequencing. Despite this species' prolonged history of small population size and highly restricted distribution, we demonstrate extensive diversity at MHC DRB with 26 alleles, whereas MHC DQB is dimorphic. We identify four DRB codons, predicted to be involved in antigen binding, that are evolving under adaptive evolution. Our data suggest diversity at DRB may be maintained by balancing selection, consistent with the role of this locus as an antigen-binding region and the species' recent history of mass mortality during a series of bacterial epizootics. Phylogenetic analyses of DQB and DRB sequences from pinnipeds and other carnivores revealed significant allelic diversity, but little phylogenetic depth or structure among pinniped alleles; thus, we could neither confirm nor refute the possibility of trans-species polymorphism in this group. The phylogenetic pattern observed however, suggests some significant evolutionary constraint on these loci in the recent past, with the pattern consistent with that expected following an epizootic event. These data may help further elucidate some of the genetic factors underlying the unusually high susceptibility to bacterial infection of the threatened NZSL, and help us to better understand the extent and pattern of MHC diversity in pinnipeds.
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Affiliation(s)
- A J Osborne
- Centre for Reproduction and Genomics, Department of Anatomy, University of Otago, Dunedin, New Zealand.
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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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Califf KJ, Ratzloff EK, Wagner AP, Holekamp KE, Williams BL. Forces shaping major histocompatibility complex evolution in two hyena species. J Mammal 2013. [DOI: 10.1644/12-mamm-a-054.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Garamszegi LZ, Nunn CL. Parasite-mediated evolution of the functional part of the MHC in primates. J Evol Biol 2010; 24:184-95. [PMID: 21091566 DOI: 10.1111/j.1420-9101.2010.02156.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The major histocompatibility complex (MHC) is a key model of genetic polymorphism, but the mechanisms underlying its extreme variability are debated. Most hypotheses for MHC diversity focus on pathogen-driven selection and predict that MHC polymorphism evolves under the pressure of a diverse parasite fauna. Several studies reported that certain alleles offer protection against certain parasites, yet it remains unclear whether variation in parasite pressure more generally covaries with allelic diversity and rates of molecular evolution of MHC across species. We tested this prediction in a comparative study of 41 primate species. We characterized polymorphism of the exon 2 of DRB region of the MHC class II. Our phylogenetic analyses controlled for the potential effects of neutral mutation rate, population size, geographic origin and body mass and revealed that nematode species richness associates positively with nonsynonymous nucleotide substitution rate at the functional part of the molecule. We failed to find evidence for allelic diversity being strongly related to parasite species richness. Continental distribution was a strong predictor of both allelic diversity and substitution rate, with higher values in Malagasy and Neotropical primates. These results indicate that parasite pressure can influence the different estimates of MHC polymorphism, whereas geography plays an independent role in the natural history of MHC.
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Affiliation(s)
- L Z Garamszegi
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Seville, Spain.
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Phagocytosis in pup and adult harbour, grey and harp seals. Vet Immunol Immunopathol 2010; 134:160-8. [DOI: 10.1016/j.vetimm.2009.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 08/21/2009] [Accepted: 08/24/2009] [Indexed: 11/23/2022]
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Major histocompatibility complex variation and evolution at a single, expressed DQA locus in two genera of elephants. Immunogenetics 2010; 62:85-100. [DOI: 10.1007/s00251-009-0413-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 11/12/2009] [Indexed: 10/20/2022]
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Low major histocompatibility complex class II DQA diversity in the Giant Panda (Ailuropoda melanoleuca). BMC Genet 2007; 8:29. [PMID: 17555583 PMCID: PMC1904234 DOI: 10.1186/1471-2156-8-29] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 06/07/2007] [Indexed: 11/24/2022] Open
Abstract
Background The giant panda (Ailuropoda melanoleuca) is one of the most endangered animals due to habitat fragmentation and loss. Although the captive breeding program for this species is now nearly two decades old, researches on the genetic background of such captive populations, especially on adaptive molecular polymorphism of major histocompatibility complex (MHC), are still limited. In this study, we characterized adaptive variation of the giant panda's MHC DQA gene by PCR amplification of its antigen-recognizing region (i.e. the exon 2) and subsequent single-strand conformational polymorphism (SSCP) and sequence analyses. Results The results revealed a low level of DQA exon 2 diversity in this rare animal, presenting 6 alleles from 61 giant panda individuals. The observed polymorphism was restricted to 9 amino acid substitutions, all of which occurred at and adjacent to positions forming the functionally important antigen-binding sites. All the samples were in Hardy-Weinberg proportions. A significantly higher rate of non-synonymous than synonymous substitutions at the antigen-binding sites indicated positive selection for diversity in the locus. Conclusion The DQA allelic diversity of giant pandas was low relative to other vertebrates. Nonetheless, the pandas exhibited more alleles in DQA than those in DRB, suggesting the alpha chain genes would play a leading role when coping with certain pathogens and thus should be included in conservation genetic investigation. The microsatellite and MHC loci might predict long-term persistence potential and short-term survival ability, respectively. Consequently, it is recommended to utilize multiple suites of microsatellite markers and multiple MHC loci to detect overall genetic variation in order to design unbiased conservation strategies.
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Genetic variation of the major histocompatibility complex (MHC class II β gene) in the threatened Gila trout, Oncorhynchus gilae gilae. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9336-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Bollmer JL, Vargas FH, Parker PG. Low MHC variation in the endangered Galápagos penguin (Spheniscus mendiculus). Immunogenetics 2007; 59:593-602. [PMID: 17457582 DOI: 10.1007/s00251-007-0221-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Accepted: 03/31/2007] [Indexed: 10/23/2022]
Abstract
The major histocompatibility complex (MHC) is one of the most polymorphic regions of the genome, likely due to balancing selection acting to maintain alleles over time. Lack of MHC variability has been attributed to factors such as genetic drift in small populations and relaxed selection pressure. The Galápagos penguin (Spheniscus mendiculus), endemic to the Galápagos Islands, is the only penguin that occurs on the equator. It relies upon cold, nutrient-rich upwellings and experiences severe population declines when ocean temperatures rise during El Niño events. These bottlenecks, occurring in an already small population, have likely resulted in reduced genetic diversity in this species. In this study, we used MHC class II exon 2 sequence data from a DRB1-like gene to characterize the amount of genetic variation at the MHC in 30 Galápagos penguins, as well as one Magellanic penguin (S. magellanicus) and two king penguins (Aptenodytes patagonicus), and compared it to that in five other penguin species for which published data exist. We found that the Galápagos penguin had the lowest MHC diversity (as measured by number of polymorphic sites and average divergence among alleles) of the eight penguin species studied. A phylogenetic analysis showed that Galápagos penguin MHC sequences are most closely related to Humboldt penguin (Spheniscus humboldti) sequences, its putative sister species based on other loci. An excess of non-synonymous mutations and a pattern of trans-specific evolution in the neighbor-joining tree suggest that selection is acting on the penguin MHC.
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Affiliation(s)
- Jennifer L Bollmer
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO, USA.
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Mainguy J, Worley K, Côté SD, Coltman DW. Low MHC DRB class II diversity in the mountain goat: past bottlenecks and possible role of pathogens and parasites. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9243-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yu W, Rusterholtz KJ, Krummel AT, Lehman N. Detection of high levels of recombination generated during PCR amplification of RNA templates. Biotechniques 2006; 40:499-507. [PMID: 16629397 DOI: 10.2144/000112124] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Recombination during the PCR amplification of DNA templates can be a serious problem for those seeking to genotype heterogeneous populations, yet a boon to those seeking to enhance variation during in vitro evolution. Here, the extent to which PCR generates chimeric full-length products was estimated using a powerful restriction fragment-length polymorphism (RFLP) assay involving the use of fluorescently labeled PCR primers. Three different RNA-encoding DNA templates were assayed: (i) one for a group I ribozyme, (ii) one for a 16S ribosomal RNA (rRNA), and (iii) one for a messenger RNA (mRNA). In all cases, the observed frequency of chimeric PCR products exceeded 20%, and longer templates appear to produce more chimeric products. Although two of these templates have the potential to form secondary structures during the PCR, this tendency does not seem to heighten recombination frequency. These results corroborate previous studies that show that the production of chimeras can be best attenuated to a certain extent by varying the extension times in PCR.
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Affiliation(s)
- Wayne Yu
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR 97207, USA
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Abstract
We obtained the nucleotide sequence for most of the major histocompatibility complex (MHC) class II DOA locus for Weddell, leopard, northern elephant, and southern elephant seals and from the coyote and compared them to all known DOA data available to date. We found generally low levels of interspecific polymorphisms, providing further support for stabilizing selection acting on the DOA locus. This suggests that DO gene products play a substantial functional role in the regulation of antigen presentation. A seven-amino-acid motif of VWRLPEF was found to be conserved across all DOA sequences and may be a DO-specific recognition element.
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Affiliation(s)
- S J Soll
- Department of Chemistry, Portland State University, Portland, OR 97207, USA
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Hammond JA, Hall AJ, Dyrynda EA. Comparison of polychlorinated biphenyl (PCB) induced effects on innate immune functions in harbour and grey seals. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2005; 74:126-38. [PMID: 15982755 DOI: 10.1016/j.aquatox.2005.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2004] [Revised: 05/05/2005] [Accepted: 05/13/2005] [Indexed: 05/03/2023]
Abstract
Polychlorinated biphenyls (PCBs) are known to have detrimental effects on the innate immune system of several mammalian species. Top predators such as marine mammals may be badly affected as PCBs can bioaccumulate in their blubber to high concentrations and previous studies have suggested that harbour seals may be particularly vulnerable to the immunotoxic effects of such contaminants. To investigate the effects of PCBs on innate immune functions in phocid seals, blood samples were collected from harbour and grey seals and exposed in vitro to a mixture of Aroclors. Separated mononuclear (PBMCs) and polymorphonuclear (PMNCs) leukocytes from each species were incubated with Aroclors (at 3 and 30 ngml(-1)) for 3 and 24 h incubation periods, after which phagocytosis, respiratory burst and cytotoxic activity were measured. The phagocytic activity of harbour seal PMNCs was decreased at both incubation times and at both Aroclor concentrations tested, but there was no effect on the grey seals. Similarly, the respiratory burst activity of harbour seals was decreased at both incubation times, but only at the higher concentration used. There were no differences in the cytotoxic activity of the PBMCs with respect to incubation times or concentrations in either species. However, differences were observed in the level of cytotoxic activity against YAC-1 target cells, with the grey seal PBMCs showing higher levels of activity. The observed differences in phagocytosis, respiratory burst and cytotoxic activity of the leukocytes following incubation with PCBs may have implications for the previously recorded differences in disease susceptibility between grey and harbour seals.
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Affiliation(s)
- John A Hammond
- School of Life Sciences, Heriot Watt University, Edinburgh EH14 4AS, UK
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