Lukacs et al. BMC Genomics 2010, 11:154 http://www.biomedcentral.com/1471-2164/11/154 Genbank: FJ969488], 184H23 [186322 bp, Genbank: FJ969489], 439J08 [218010 bp, Genbank: FJ969490], 68O19 [240893 bp, Genbank: GQ505860], 439H13 [152251 bp, Genbank: GQ505859] and 129P21 [202799 bp, Genbank: GQ505858]. 222F07 and 357C09 are only partially sequenced using 454 and thus not sent to Genbank. Genomic surroundings of Atlantic salmon U-, S-, and Z- lineage genes We have used nomenclature with IA covering the UBA locus region and IB for the duplicated UCA/UDA region. New genes identified here will be named accord- ingly; the IA genes are given an extension of a (e.g. RING1a) and the IB genes have an extension of b (e.g. RING1b). Previously identified MHC class I molecules from the Z-lineage have been termed ZE with allelic extensions. We here propose that the four Z-lineage loci should be named with three letters as used for other MHC class I genes i.e ZAA; first letter - describing line- age, second letter - increasing letters A, B, C and D to reflect locus and the last letter - A for alpha chain. A MHC class I gene residing in 114L13 was originally defined as UAA in rainbow trout by Shum [16]. Here we rename this gene to SAA to visualize the fact that this molecule shows very low identity to other U-lineage molecules (this nomenclature will also be used for the rainbow trout molecule, i.e. Onmy-SAA). We propose that the lineage should be designated as S as this class I lineage was first described in salmonids. The gene orga- nization of U-, S- and Z-lineage containing regions are shown in Figure 1. 439J08 represents an allelic version of the IB region residing on LG3 thus denoted LG3-2. Genes for ZAA, ATF6a and TNXBa were found in the extended IA region. The IB region was extended with genes for UGA, RING1b, RPS18b, VPS52b, VHSVb, ATF6b, TNXBb, PSMB7, CENPA, ZBA, ZCA, ZDA, ATAD2, ZHX1, ZHX2. We also found four almost iden- tical genes in the extended IB region which had several EST matches [ex. Genbank: EG844714] and we define them as Hypothetical (Figure 1) as their functions are currently unknown. The three first genes were 100% identical on a protein level, while the last gene con- tained one amino acid substitution. Genes identified in 114L13 on LG10 were SAA, VWA5A, VWA5A-homolog, AKT2, and in 184H23 two UHA genes (UHA1 and UHA2) were identified in addition to AhR1, AhR2, AGPAT3 and PDXK. The gene TNXB was found in both the IA and IB regions, being an Atlantic salmon ortholog of a gene residing in the extended human MHC class III region. TNXB is a member of the tenascin family of extracellu- lar matrix glycoproteins, which has anti-adhesive effects and functions in matrix maturation during wound Page 4 of 17 healing [19]. ATF6 was also identified in both regions. The human ATF6-beta (CREBL1) is located close to TNXB on chromosome 6, while ATF6-alpha is located on chromosome 1. ATF6-beta functions as a transcrip- tion factor in the unfolded protein response pathway during endoplasmatic reticulum stress [19]. We also found genes in the IB region that we have pre- viously found in the IA region; RING1, RPS18, VPS52 and VHSV. Some of these genes were quite divergent from their IA counterparts with 91%, 100%, 75% and 70% amino acid identity respectively. VPS52 in the IB region is probably a pseudogene, since the gene only consisted of 293 amino acids (aa) compared to 773 aa in IA. How- ever, VPS52 showed 100% identity toward a predicted CDS in Genbank [ACM08348], thus indicating that this IB genes is still expressed. VPS52 in humans is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. The ATAD2, ZHX1 and ZHX2 genes identified in the extended IB region have an identical gene orientation as that found on human chromosome 8. ATAD2 belongs to a large family of ATPases and these proteins often perform chaperone-like functions that assist in the assembly, operation and disassembly of protein com- plexes [19]. Members of the zinc fingers and homeo- boxes gene family (i.e. ZHX1 and ZHX2) are nuclear homodimeric transcriptional repressors that interact with the A subunit of nuclear factor-Y (NF-YA) and contain two C2H2-type zinc fingers and five homeobox DNA-binding domains [19]. We found a cDNA match for PSMB7 (proteasome subunit Z; [Genbank: BT046757]) which is a subunit of the 20S proteasome subunit complex in the IB region. Perhaps a duplicated PSMB7 gene exists in Atlantic sal- mon as another sequence [Genbank: ACI68005] showed 68% identity on the protein level. PSMB7 is located on chromosome 9 in humans and on chromosome 21 in zebrafish (i.e. the gene is not MHC linked) as the human and zebrafish MHC region resides on chr.6 and chr.19 respectively. Genes identified in the UHA and SAA positive BACs were two AhR genes, AGPAT3 and PDXK in 184H23 and VWA5A and AKT2 in 114L13. The AhR2 gene shows high similarity towards a Genbank mRNA sequence ([Genbank: AY219864]; more than 99% iden- tity), but lacks exon1 and 2. Hansson et al described three Atlantic salmon AhR2 genes (alpha, beta and gamma) and two AhR1 genes (alpha and beta), all con- taining a minimum of 11 exons [20]. Either the two lacking AhR2 exons are located upstream of 184H23 or this gene is a pseudogene with a functional copy some- where else. We found no matching EST for the pre- dicted AhR1 gene which we then define as a pseudogene.