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Background  The Major Histocompatibility Complex (MHC) is a genomic region containing genes with crucial roles in immune responses. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. To counteract the high variability of pathogens, the MHC evolved into a region of considerable heterogeneity in its organization, number and extent of polymorphism. Studies of MHCs in different model species contribute to our understanding of mechanisms of immunity, diseases and their evolution. Camels are economically important domestic animals and interesting biomodels. Three species of Old World camels have been recognized: the dromedary ( Camelus dromedarius ), Bactrian camel ( Camelus bactrianus ) and the wild camel ( Camelus ferus ). Despite their importance, little is known about the MHC genomic region, its organization and diversity in camels. The objectives of this study were to identify, map and characterize the MHC region of Old World camelids, with special attention to genetic variation at selected class MHC II loci.    Results  Physical mapping located the MHC region to the chromosome 20 in Camelus dromedarius. Cytogenetic and comparative analyses of whole genome sequences showed that the order of the three major sub-regions is “Centromere - Class II – Class III – Class I”.  DRA, DRB, DQA  and  DQB  exon 2 sequences encoding the antigen binding site of the corresponding class II antigen presenting molecules showed high degree of sequence similarity and extensive allele sharing across the three species. Unexpectedly low extent of polymorphism with low numbers of alleles and haplotypes was observed in all species, despite different geographic origins of the camels analyzed. The  DRA  locus was found to be polymorphic, with three alleles shared by all three species.  DRA  and  DQA  sequences retrieved from ancient DNA samples of  Camelus dromedarius  suggested that additional polymorphism might exist.    Conclusions  This study provided evidence that camels possess an MHC comparable to other mammalian species in terms of its genomic localization, organization and sequence similarity. We described ancient variation at the  DRA  locus, monomorphic in most species. The extent of molecular diversity of MHC class II genes seems to be substantially lower in Old World camels than in other mammalian species.Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2500-1) contains supplementary material, which is available to authorized users.

The major histocompatibility complex in Old World camelids and low polymorphism of its class II genes