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MHC class II genes in the European badger (Meles meles): characterization, patterns of variation, and transcription analysis

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Abstract

The major histocompatibility complex (MHC) comprises many genes, some of which are polymorphic with numerous alleles. Sequence variation among alleles is most pronounced in exon 2 of the class II genes, which encodes the α1 and β1 domains that form the antigen-binding site (ABS) for the presentation of peptides. The MHC thus plays an important role in pathogen defense. European badgers (Meles meles) are a good species in which to study the MHC, as they harbor a variety of pathogens. We present the first characterization of MHC class II genes, isolated from genomic DNA (gDNA) and complementary DNA (cDNA), in the European badger. Examination of seven individuals revealed four DRB, two DQB, two DQA, and two DRA putatively functional gDNA sequences. All of these sequences, except DRA, exhibited high variability in exon 2; DRB had the highest variability. The ABS codons demonstrated high variability, due potentially to balancing selection, while non-ABS codons had lower variability. Positively selected sites were detected in DRB and DQA. Phylogenetic analysis demonstrated trans-species polymorphism of class II genes. Comparison with cDNA from whole blood revealed that only DRB had a transcription pattern reflecting the alleles that were present in the gDNA, while the other three genes had disparities between gDNA and cDNA. Only one sequence was transcribed, even though two gDNA sequences were present, from each of both DQB and DRA. Our characterization of badger MHC sequences forms a basis for further studies of MHC variability, mate choice, and pathogen resistance in this, and other, species.

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Acknowledgments

We thank the Wytham Woods badger team, especially Geetha Annavi, Christina Buesching, Stephen Ellwood, and Pierre Nouvellet, for assistance with badger trapping. We thank Geetha Annavi for providing relatedness data. We also thank Deborah Dawson, Gavin Horsburgh Andy Krupa, and Maria-Elena Mannarelli for assistance with laboratory work. The T. taxus samples were generously provided by Alain Frantz and Emily Latch. We thank two anonymous reviewers for their helpful comments on the manuscript. This research was supported by the UK NERC Biomolecular Analysis Facility, the Croucher Foundation (Hong Kong), and the Netherlands Organisation for Scientific Research. All animal handling was carried out under Natural England Licence, currently 20104655, and UK Home Office License PPL 30/2835.

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  1. Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon, Oxfordshire, OX13 5QL, UK

    Yung Wa Sin, Chris Newman & David W. Macdonald

  2. Natural Environment Research Council (NERC) Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK

    Yung Wa Sin, Hannah L. Dugdale & Terry Burke

  3. Behavioural Ecology and Self-Organization, University of Groningen, PO Box 11103, 9700 CC, Groningen, Netherlands

    Hannah L. Dugdale

  4. Theoretical Biology, University of Groningen, PO Box 11103, 9700 CC, Groningen, Netherlands

    Hannah L. Dugdale

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  1. Yung Wa Sin
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Sin, Y.W., Dugdale, H.L., Newman, C. et al. MHC class II genes in the European badger (Meles meles): characterization, patterns of variation, and transcription analysis. Immunogenetics 64, 313–327 (2012). https://doi.org/10.1007/s00251-011-0578-9

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