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Background  Bats are an extremely successful group of mammals and possess a variety of unique characteristics, including their ability to co-exist with a diverse range of pathogens. The major histocompatibility complex (MHC) is the most gene dense and polymorphic region of the genome and MHC class II (MHC-II) molecules play a vital role in the presentation of antigens derived from extracellular pathogens and activation of the adaptive immune response. Characterisation of the MHC-II region of bats is crucial for understanding the evolution of the MHC and of the role of pathogens in shaping the immune system.    Results  Here we describe the relatively contracted MHC-II region of the Australian black flying-fox ( Pteropus alecto ), providing the first detailed insight into the MHC-II region of any species of bat. Twelve MHC-II genes, including one locus ( DRB2 ) located outside the class II region, were identified on a single scaffold in the bat genome. The presence of a class II locus outside the MHC-II region is atypical and provides evidence for an ancient class II duplication block. Two non-classical loci,  DO  and  DM  and two classical,  DQ  and  DR  loci, were identified in  P. alecto . A putative classical,  DPB  pseudogene was also identified. The bat’s antigen processing cluster, though contracted, remains highly conserved, thus supporting its importance in antigen presentation and disease resistance.    Conclusions  This detailed characterisation of the bat MHC-II region helps to fill a phylogenetic gap in the evolution of the mammalian class II region and is a stepping stone towards better understanding of the immune responses in bats to viral, bacterial, fungal and parasitic infections.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3760-0) contains supplementary material, which is available to authorized users.

Insights into the ancestral organisation of the mammalian MHC class II region from the genome of the pteropid bat, Pteropus alecto