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Transcriptome-based primer design: bank vole MHC class I

posted Nov 4, 2016, 4:33 AM by Magdalena Migalska
Although high-throughput sequencing has increasingly been used for genotyping families of co-amplifying genes, its potential to facilitate the initial characterisation of such genes in non-model species has not been explored. In our recent article in Heredity we found that, while de novo transcriptome assembly of major histocompatibility complex (MHC) class I genes does not reconstruct sequences of individual alleles, it allows the identification of conserved regions for PCR primer design.

Using the newly designed primers, we characterised for the first time MHC class I sequences in an Arvicolinae rodent, the bank vole (Myodes glareolus). We showed high allelic diversity and inter-individual variation in the number of expressed loci. Phylogenetic analysis revealed a lack of orthology to MHC I of other Cricetidae, which is consistent with the high gene turnover of this region. Strong signatures of positive selection were found for eight amino acid sites, most of which are inferred to bind antigens in human MHC, indicating conservation of structure despite rapid sequence evolution.