Comprehensive Analysis of MHC Class I Genes from the U-, S-, and Z-Lineages in Atlantic Salmon

Background: We have previously sequenced more than 500 kb of the duplicated MHC class I regions in Atlanticsalmon. In the IA region we identified the loci for the MHC class I gene Sasa-UBA in addition to a soluble MHCclass I molecule, Sasa-ULA. A pseudolocus for Sasa-UCA was identified in the nonclassical IB region. Both regionscontained genes for antigen presentation, as wells as orthologues to other genes residing in the human MHCregion.Results: The genomic localisation of two MHC class I lineages (Z and S) has been resolved. 7 BACs weresequenced using a combination of standard Sanger and 454 sequencing. The new sequence data extended the IAregion with 150 kb identifying the location of one Z-lineage locus, ZAA. The IB region was extended with 350 kbincluding three new Z-lineage loci, ZBA, ZCA and ZDA in addition to a UGA locus. An allelic version of the IB regioncontained a functional UDA locus in addition to the UCA pseudolocus. Additionally a BAC harbouring two MHCclass I genes (UHA) was placed on linkage group 14, while a BAC containing the S-lineage locus SAA (previouslyknown as UAA) was placed on LG10. Gene expression studies showed limited expression range for all class I geneswith exception of UBA being dominantly expressed in gut, spleen and gills, and ZAA with high expression in blood.Conclusion: Here we describe the genomic organization of MHC class I loci from the U-, Z-, and S-lineages inAtlantic salmon. Nine of the described class I genes are located in the extension of the duplicated IA and IBregions, while three class I genes are found on two separate linkage groups. The gene organization of the tworegions indicates that the IB region is evolving at a different pace than the IA region. Expression profiling,polymorphic content, peptide binding properties and phylogenetic relationship show that Atlantic salmon has onlyone MHC class Ia gene (UBA), in addition to a multitude of nonclassical MHC class I genes from the U-, S- andZ-lineages.