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

Jessica Hacking, Tessa Bradford, Kelly Pierce, Michael Gardner

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)97-117
Number of pages21
JournalTransactions of the Royal Society of South Australia
Volume143
Issue number1
DOIs
Publication statusPublished - May 2019

Keywords

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

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