Diversity at immune loci such as the Major Histocompatibility Region (MHC) is often used as a proxy for determining potential immunological health of a population and the chance that a given population will be able to adapt to the emergence of novel pathogens or disease threats. However, efforts to characterise sequence diversity at these loci have been hampered by a need for prior sequence data. Furthermore, despite efforts to generate genomic sequence data for a wide variety of vertebrate species (e.g. the G10K and B10K efforts), highly complex regions such as the MHC and immunoglobulin loci remain difficult to assemble.
We are combining targeted sequence capture arrays with a combination of long and short read sequencing approaches to improve contiguity over these genomic regions for existing genomes and extending the use of these technologies to characterise the MHC of species without a reference genome. Here we will discuss the use of sequence capture arrays for conservation immunogenetics, and their potential for use in cross-species immunogenetic studies. We will present pilot studies for determination of MHC haplotypes in the well characterised domestic pig model, and discuss the application to endangered mustelids.