Lukacs et al. BMC Genomics 2010, 11:154 http://www.biomedcentral.com/1471-2164/11/154 4. Stet RJ, Kruiswijk CP, Saeij JP, Wiegertjes GF: Major histocompatibility genes in cyprinid fishes: theory and practice.Immunol Rev 1998, 166:301-316. 5. Kruiswijk CP, Hermsen TT, Westphal AH, Savelkoul HF, Stet RJ: A novel functional class I lineage in zebrafish (Danio rerio), carp (Cyprinus carpio), and large barbus (Barbus intermedius) showing an unusual conservation of the peptide binding domains.J Immunol 2002, 169:1936-1947. 6. Hashimoto K, Nakanishi T, Kurosawa Y: Isolation of carp genes encoding major histocompatibility complex antigens.Proc Natl Acad Sci USA 1990, 87:6863-6867. 7. Grimholt U, Drablos F, Jorgensen SM, Hoyheim B, Stet RJ: The major histocompatibility class I locus in Atlantic salmon (Salmo salar L.): polymorphism, linkage analysis and protein modelling.Immunogenetics 2002, 54:570-581. 8. Phillips RB, Zimmerman A, Noakes MA, Palti Y, Morasch MR, Eiben L, et al: Physical and genetic mapping of the rainbow trout major histocompatibility regions: evidence for duplication of the class I region. Immunogenetics 2003, 55:561-569. 9. Kassahn KS, Dang VT, Wilkins SJ, Perkins AC, Ragan MA: Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates.Genome Res 2009, 19:1404-1418. 10. Allendorf FW, Thorgaard GH: Tetraploidy and the evolution of salmonid fishes.Evolutionary Genetics of Fishes New York: PlenumTurner BJ 1984, 1-53. 11. Shiina T, Dijkstra JM, Shimizu S, Watanabe A, Yanagiya K, Kiryu I, et al: Interchromosomal duplication of major histocompatibility complex class I regions in rainbow trout (Oncorhynchus mykiss), a species with a presumably recent tetraploid ancestry.Immunogenetics 2005, 56:878-893. 12. Hansen JD, Strassburger P, Thorgaard GH, Young WP, Du PL: Expression, linkage, and polymorphism of MHC-related genes in rainbow trout, Oncorhynchus mykiss.J Immunol 1999, 163:774-786. 13. Lukacs MF, Harstad H, Grimholt U, Beetz-Sargent M, Cooper GA, Reid L, et al: Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon (Salmo salar).BMC Genomics 2007, 8:251. 14. Kiryu I, Dijkstra JM, Sarder RI, Fujiwara A, Yoshiura Y, Ototake M: New MHC class Ia domain lineages in rainbow trout (Oncorhynchus mykiss) which are shared with other fish species.Fish Shellfish Immunol 2005, 18:243-254. 15. Miller KM, Li S, Ming TJ, Kaukinen KH, Schulze AD: The salmonid MHC class I: more ancient loci uncovered.Immunogenetics 2006, 58:571-589. 16. Shum BP, Rajalingam R, Magor KE, Azumi K, Carr WH, Dixon B, et al: A divergent non-classical class I gene conserved in salmonids. Immunogenetics 1999, 49:479-490. 17. Danzmann RG, Davidson EA, Ferguson MM, Gharbi K, Koop BF, Hoyheim B, et al: Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon).BMC Genomics 2008, 9:557. 18. Phillips RB, Keatley KA, Morasch MR, Ventura AB, Lubieniecki KP, Koop BF, et al: Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: Conservation of large syntenic blocks corresponding to whole chromosome arms in rainbow trout (Oncorhynchus mykiss).BMC Genet 2009, 10:46. 19. NCBI Entrez Gene. Internet 2009 [http://www.ncbi.nlm.nih.gov/sites/entrez? db=gene]. 20. Hansson MC, Wittzell H, Persson K, von Schantz T: Characterization of two distinct aryl hydrocarbon receptor (AhR2) genes in Atlantic salmon (Salmo salar) and evidence for multiple AhR2 gene lineages in salmonid fish.Gene 2003, 303:197-206. 21. Martin ES, Cesari R, Pentimalli F, Yoder K, Fishel R, Himelstein AL, et al: The BCSC-1 locus at chromosome 11q23-q24 is a candidate tumor suppressor gene.Proc Natl Acad Sci USA 2003, 100:11517-11522. 22. Dijkstra JM, Kiryu I, Yoshiura Y, Kumanovics A, Kohara M, Hayashi N, et al: Polymorphism of two very similar MHC class Ib loci in rainbow trout (Oncorhynchus mykiss).Immunogenetics 2006, 58:152-167. 23. Hashimoto K, Okamura K, Yamaguchi H, Ototake M, Nakanishi T, Kurosawa Y: Conservation and diversification of MHC class I and its related molecules in vertebrates.Immunol Rev 1999, 167:81-100. 24. Steinke D, Salzburger W, Meyer A: Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs.J Mol Evol 2006, 62:772-784. 25. Blast: Basic Local Alignment Search Tool. Internet 2009. Page 16 of 17 26. Consortium for Genomics Research on All Salmon. Internet 2009 [http://web.uvic.ca/cbr/grasp/]. 27. Koop BF, von Schalburg KR, Leong J, Walker N, Lieph R, Cooper GA, et al: A salmonid EST genomic study: genes, duplications, phylogeny and microarrays.BMC Genomics 2008, 9:545. 28. Kaufman J, Salomonsen J, Flajnik M: Evolutionary conservation of MHC class I and class II molecules–different yet the same.Semin Immunol 1994, 6:411-424. 29. Madden DR: The three-dimensional structure of peptide-MHC complexes. Annu Rev Immunol 1995, 13:587-622. 30. Saper MA, Bjorkman PJ, Wiley DC: Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 A resolution.J Mol Biol 1991, 219:277-319. 31. Moore LJ, Somamoto T, Lie KK, Dijkstra JM, Hordvik I: Characterisation of salmon and trout CD8alpha and CD8beta.Mol Immunol 2005, 42:1225-1234. 32. Contini P, Ghio M, Poggi A, Filaci G, Indiveri F, Ferrone S, et al: Soluble HLA-A,-B,-C and -G molecules induce apoptosis in T and NK CD8+ cells and inhibit cytotoxic T cell activity through CD8 ligation.Eur J Immunol 2003, 33:125-134. 33. Yao YQ, Barlow DH, Sargent IL: Differential expression of alternatively spliced transcripts of HLA-G in human preimplantation embryos and inner cell masses.J Immunol 2005, 175:8379-8385. 34. Rebmann V, Pfeiffer K, Passler M, Ferrone S, Maier S, Weiss E, et al: Detection of soluble HLA-G molecules in plasma and amniotic fluid. Tissue Antigens 1999, 53:14-22. 35. Fournel S, guerre-Girr M, Huc X, Lenfant F, Alam A, Toubert A, et al: Cutting edge: soluble HLA-G1 triggers CD95/CD95 ligand-mediated apoptosis in activated CD8+ cells by interacting with CD8.J Immunol 2000, 164:6100-6104. 36. Children’s Hospital Oakland Research Institute (CHORI). Internet 2009 [http://bacpac.chori.org/]. 37. Thorsen J, Zhu B, Frengen E, Osoegawa K, de Jong PJ, Koop BF, et al: A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects.BMC Genomics 2005, 6:50-60. 38. Ng SH, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, et al: A physical map of the genome of Atlantic salmon, Salmo salar.Genomics 2005, 86:396-404. 39. Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities.Genome Res 1998, 8:186-194. 40. Ewing B, Hillier L, Wendl MC, Green P: Base-calling of automated sequencer traces using phred. I. Accuracy assessment.Genome Res 1998, 8:175-185. 41. Phrap; a program for assembling shotgun DNA sequences. Internet 2009 [http://www.phrap.org/]. 42. Gordon D, Abajian C, Green P: Consed: a graphical tool for sequence finishing.Genome Res 1998, 8:195-202. 43. Gordon D, Desmarais C, Green P: Automated finishing with autofinish. Genome Res 2001, 11:614-625. 44. Digit Web Server. Internet 2009 [http://hgp.gsc.riken.go.jp/index.php/ Program_DIGIT]. 45. Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA.J Mol Biol 1997, 268:78-94. 46. Sonnhammer EL, Durbin R: A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis.Gene 1995, 167:GC1-10. 47. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I: VISTA: computational tools for comparative genomics.Nucleic Acids Res 2004, 32: W273-W279. 48. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool.J Mol Biol 1990, 215:403-410. 49. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.Nucleic Acids Res 1997, 25:3389-3402. 50. Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W: A computer program for aligning a cDNA sequence with a genomic DNA sequence.Genome Res 1998, 8:967-974. 51. Wheelan SJ, Church DM, Ostell JM: Spidey: a tool for mRNA-to-genomic alignments.Genome Res 2001, 11:1952-1957. 52. GRASP repeatmasker. Internet 2009 [http://lucy.ceh.uvic.ca/repeatmasker/ cbr_repeatmasker.py].