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Background  The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family  Equidae  includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II  DRA  and  DQA  loci have received attention, the genetic diversity and effects of selection on  DRB  and  DQB  loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II  DRB  and  DQB  loci in the  Equidae  family.    Results  Three  DRB  and two  DQB  genes were identified in the genomes of all equids. The genes  DRB2 ,  DRB3  and  DQB3  showed high sequence conservation, while polymorphisms were more frequent at  DRB1  and  DQB1  across all species analyzed.  DQB2  was not found in the genome of the Asiatic asses  Equus hemionus kulan  and  E. h. onager . The bioinformatic analysis of non-zero-coverage-bases of  DRB  and  DQB  genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for  DRB1 ,  DRB2, DQB1  and  DQB2  genes. Trans-species allele sharing was identified in all genes except  DRB1 . Site-specific selection analysis predicted genes evolving under positive selection both at  DRB  and  DQB  loci. No selected amino acid sites were identified in  DQB3 .    Conclusions  The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II  DRB / DQB  sub-regions in the  Equidae .

Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae