Conservation of promoter, coding and intronic regions of the non-classical MHC class II DYA gene suggests evolution under functional constraints

The major histocompatibility complex (MHC) in ruminants contains a unique pair of class II genes (DYA and DYB) of unknown function. As functional genes show higher levels of nucleotide conservation than pseudogenes we compared the DYA genes from sheep and cattle, two species which diverged from a common ancestor approximately 20 million years ago. Comparative analysis identified levels of nucleotide conservation in immediate promoter (97%), coding (94%) and intronic regions (91%) comparable with functional MHC genes. The Ovar-DYA transcript revealed an open reading frame encoding a 288 amino acid protein compared with a 253 amino acid protein associated with the BoLA-DYA transcript. A dinucleotide deletion in exon 4 of the Ovar-DYA transcript combined with alternative exon 5 splice sites introduces unusual diversity to the cytoplasmic domain of the Ovar-DY alpha polypeptide. The degree of conservation between these class II MHC genes is consistent with evolution under purifying selection suggesting that these genes retain a unique function in ruminants.