Lukacs et al. BMC Genomics 2010, 11:154 http://www.biomedcentral.com/1471-2164/11/154 HLA-G. Additionally lipid binders like CD1, non-ligand binders like MIC-A/B and HFE, and other molecules like MR1, ZAG, FcRn and ULBP have features of MHC class Ib character. An emerging view on the MHC class Ib molecules are their prominent role bridging the innate and acquired immunity [2]. Teleost fishes also display a wide variety of MHC class I molecules, and earlier reports classify these genes into the U-, Z- and L-lineage based on evolutionary relation- ship [3,4]. However information regarding polymorphic content, expression patterns and ligand binding are mostly lacking for these MHC class I genes. The broad U-lineage is present in most teleosts, covering both MHC class Ia and Ib sequences. Z-lineage molecules have now been identified in a multitude of teleosts [4-6]. L-lineage molecules are so far only found in sal- monids and cyprinids, and represent highly divergent class Ib genes [3]. All teleost fishes have their MHC class I and II regions located on different linkage groups [7,8], an event thought to have emerged by a genome duplication event early in the teleost evolution [9]. A unique salmo- nid specific genome duplication event occurring 60 mya [10,11] resulted in a duplicated MHC class I region residing on different chromosomes in salmonids [8,12] and the two regions are denoted class IA and class IB [11,13]. The classical UBA locus in addition to a ULA locus lacking a transmembrane region reside in the IA region, while a class Ib pseudolocus UCA was found in the Atlantic salmon IB region [13]. This is in contrast to what was found in rainbow trout, where the IA region only contained a UBA locus and the IB region contained three expressed nonclassical genes (UCA, UDA and UEA) in addition to one UFA pseudolocus [11]. Studies by Kiryu et al and Miller et al [14,15] revealed the existence of additional MHC class I loci in salmonids (UGA, UHA and ZE), although the genomic location of these loci remained unclear. Additionally, a class I molecule first reported by Shum et al. [16], was defined as if belonging to the U-lineage (UAA), despite its phylogenetic divergence from traditionally U-lineage molecules. An equally divergent class I molecule defined as the L-lineage was reported by Dijkstra et al [3] in rainbow trout, Atlantic salmon, zebrafish and fathead minnow. Here we describe the genomic organization of U-, Z-, and S-lineage MHC class I genes in Atlantic salmon, where SAA (S-lineage) replaces the UAA nomenclature because of its distant phylogenetic relationship to any other class I molecules. Additionally expression profil- ing, polymorphism, peptide binding properties and phylogenetic relationship were studied to further charac- terize the MHC class I molecules. Page 2 of 17 Results and discussion Characterization and sequencing of BAC clones An Atlantic salmon BAC library was screened with probes for UHA, UAA and ZE, and positive BACs were ordered into contigs using restriction fragment analysis together with GRASP HindIII fingerprint information. After PCR verification that the BACs contained sequence of interest, 184H23 and 114L13 were chosen as sequencing candidates for UHA and UAA respec- tively. We rename UAA to SAA (see arguments below) and will use this definition throughout the paper. The ZE positive BACs clustered into two contigs and were shown to represent extensions of sequenced BACs in the duplicated MHC class I regions based on finger- print data [13]. 129P21 was chosen from the IA region, while 68O19 for the IB region. 439H13 was later cho- sen and sequenced to obtain a continuous sequence of the IB region and the overlapping sequence of 439H13 and 68O19 showed 100% sequence identity over 11055 bp. An overview of the genomic position of all sequenced BACs covering the IA and IB regions is shown in Figure 1. In our previous study we identified two BACs (439J08, 357C09) positive for an allelic version of the IB region since PCR analysis revealed that these two BAC clones possessed different UCA-like sequences [13]. Thus they were chosen as sequencing candidates. Additionally we chose to sequence a BAC that was PCR positive for UGA (222F07). The BACs 439J08, 222F07, 184H23, 114L13 and 357C09 were initially sequenced using 454 technologies. Later Sanger shotgun libraries were made and sequenced to close gaps for 439J08, 114L13 and 184H23. The remaining BAC clones 129P21, 439H13 and 68O19 were subjected to Sanger sequencing only. Our additional sequence data i.e. 129P21 extends the Atlantic salmon IA region to cover 650 kb, while the IB region being extended with 222F07, 439H13 and 68O19 now covers 870 kb. 439J08 was indeed an allelic variant of the previously IB representative 8I14, with an inser- tion of 50 kb that increased the total described IB region to 920 kb. To identify the genomic location of the SAA and UHA positive BACs they were mapped in a mapping reference panel to linkage groups 10 and linkage group 14 respectively [17] (Additional File 1). The IA region containing the classical locus UBA resides on linkage group 15 while the nonclassical IB region is located on linkage group 3 [13]. An association between linkage groups and chromosomes can be found in Phillips et al [18]. The BAC clones were submitted to Genbank and have the following accession numbers 114L13 [134379 bp,