Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon

Abstract

<p>Abstract</p> <p>Background</p> <p>We have previously sequenced more than 500 kb of the duplicated MHC class I regions in Atlantic salmon. In the IA region we identified the loci for the MHC class I gene <it>Sasa-UBA </it>in addition to a soluble MHC class I molecule, <it>Sasa-ULA</it>. A pseudolocus for <it>Sasa-UCA </it>was identified in the nonclassical IB region. Both regions contained genes for antigen presentation, as wells as orthologues to other genes residing in the human MHC region.</p> <p>Results</p> <p>The genomic localisation of two MHC class I lineages (Z and S) has been resolved. 7 BACs were sequenced using a combination of standard Sanger and 454 sequencing. The new sequence data extended the IA region with 150 kb identifying the location of one Z-lineage locus, <it>ZAA</it>. The IB region was extended with 350 kb including three new Z-lineage loci, <it>ZBA</it>, <it>ZCA </it>and <it>ZDA </it>in addition to a <it>UGA </it>locus. An allelic version of the IB region contained a functional <it>UDA </it>locus in addition to the <it>UCA </it>pseudolocus. Additionally a BAC harbouring two MHC class I genes (UHA) was placed on linkage group 14, while a BAC containing the S-lineage locus <it>SAA </it>(previously known as <it>UAA</it>) was placed on LG10. Gene expression studies showed limited expression range for all class I genes with exception of <it>UBA </it>being dominantly expressed in gut, spleen and gills, and <it>ZAA </it>with high expression in blood.</p> <p>Conclusion</p> <p>Here we describe the genomic organization of MHC class I loci from the U-, Z-, and S-lineages in Atlantic salmon. Nine of the described class I genes are located in the extension of the duplicated IA and IB regions, while three class I genes are found on two separate linkage groups. The gene organization of the two regions 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 only one MHC class Ia gene (<it>UBA</it>), in addition to a multitude of nonclassical MHC class I genes from the U-, S- and Z-lineages.</p