Acrocephalus schoenobaenus MHC class I ultra-deep sequencing genotyping

Birds in the genus Acrocephalus have dozens of co-amplifying MHC class I genes and here we attempt to resolve complex genotypes in the sedge warbler (Acrocephalus schoenobaenus) using ultra-deep Illumina Mi-Seq sequencing. We sequenced exon 3 of MHC class I genes in 24 individuals in triplicate and used this data to test the effect of amplicon coverage (range: 500-20000 reads per amplicon) on the repeatability of genotyping using four different genotyping approaches.