De novo genotyping of the major histocompatibility complex in an Australian dragon lizard, Ctenophorus decresii

ABSTRACT

The major histocompatibility complex (MHC) is a hypervariable gene family that plays an essential role in the recognition of pathogens and immune response. Research on the reptilian MHC has lagged behind other vertebrate groups. Here, we genotyped individuals of an Australian agamid lizard species at MHC class I loci using a recently developed clustering method and family group data. Our method allowed identification of low amplification efficiency alleles and estimation of both type I and II genotyping error rates. The number of MHC class I alleles per individual varied within populations and together with allele segregation patterns, suggests either natural copy number variation or allele dropout. Genotypes from individuals across five populations revealed shared alleles among populations and low allelic diversity in an island population. Finally, we identified sites under selection and designated them putative peptide binding regions. Our results provide a foundation for future work on the MHC class I region of agamid lizards.

KEYWORDS:

• Agamidae
• next-generation amplicon sequencing
• allele segregation
• AmpliSAT
• peptide binding region
• copy number variation
• MHC
• Ctenophorus decresii
• genotyping error

Acknowledgements

All methods were approved by the Flinders University Animal Welfare Committee (E379) and the Department of Environment, Water and Natural Resources (U26225). Fieldwork at the Yourambulla Caves Aboriginal Heritage site in Hawker was approved by the Adnyamathanha Traditional Lands Association. We thank volunteers and colleagues that helped with fieldwork. We also thank Terry Bertozzi for helpful discussions. This work was funded by the Holsworth Wildlife Research endowment, Nature Foundation of South Australia and American Society for the Study of Amphibians and Reptiles, awarded to JH.

Disclosure statement

No potential conflict of interest was reported by the authors.

Supplemental material

Supplementary data for this article can be accessed here.

Additional information

Funding

This work was funded by the Holsworth Wildlife Research endowment, Nature Foundation of South Australia and American Society for the Study of Amphibians and Reptiles, awarded to JH.