BMC Genomics 2005, 6:152 http://www.biomedcentral.com/1471-2164/6/152 tion. Zebrafish and human gene names are given in lower and upper case, respectively. The zebrafish source DNA for the whole-genome assem- bly was acquired from approximately 1000 five day old embryos. This has resulted in possible misassemblies due to polymorphisms between sequences, different haplo- types, and difficulties with the assembly of duplicated genes and regions, in particular with many highly homol- ogous MHC genes that have arisen by duplication. Where possible, finished clones [e.g. EMBL:AL672216, EMBL:AL672151, EMBL:AL672185, EMBL:AL672164, EMBL:AL672176] were used to study the short-range link- age of genes in preference to the Ensembl whole-genome assembly. Alternative mapping information, for compari- son and validity of the in-silico approach used during this study, was obtained from the Zebrafish Information Net- work (ZFIN) [45] and published scientific literature. Authors' contributions JS carried out the analysis on the whole-genome assembly and drafted the manuscript. FF contributed materials and data. SB conceived the study and contributed towards the preparation of the manuscript. Note added in proof At least one of the genes stated to be missing in assembly Zv4 is present in assembly Zv5 which was released on October 2005. Acknowledgements We like to thank all members of the sequencing department and zebrafish project group at the Sanger Institute [43] and K. Belov for comments. We would like to acknowledge J. Klein for providing genomic clones used in this study. JS and SB were supported by the Wellcome Trust. References MHC Sequencing Consortium: Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortium. Nature 1999, 401:921-923. Parham P: Virtual reality in the MHC. Immunol Rev 1999, 167:5-15. Marchalonis JJ, Schluter SF: On the relevance of invertebrate recognition and defence mechanisms to the emergence of the immune response of vertebrates. Scand J Immunol 1990, 32:13-20. Milner CM, Campbell RD: Genetic organization of the human MHC class III region. Front Biosci 2001, 6:D914-26. Kelley J, Walter L, Trowsdale J: Comparative genomics of major histocompatibility complexes. Immunogenetics 2005, 56:683-695. Kaufman J, Milne S, Gobel TW, Walker BA, Jacob JP, Auffray C, Zoorob R, Beck S: The chicken B locus is a minimal essential major histocompatibility complex. Nature 1999, 401:923-925. Shiina T, Shimizu S, Hosomichi K, Kohara S, Watanabe S, Hanzawa K, Beck S, Kulski JK, Inoko H: Comparative genomic analysis of two avian (quail and chicken) MHC regions. J Immunol 2004, 172:6751-6763. Freeman-Gallant CR, Johnson EM, Saponara F, Stanger M: Variation at the major histocompatibility complex in Savannah spar- rows. Mol Ecol 2002, 11:1125-1130. Terado T, Okamura K, Ohta Y, Shin DH, Smith SL, Hashimoto K, Takemoto T, Nonaka MI, Kimura H, Flajnik MF, Nonaka M: Molecu- 1. 2. 3. 4. 5. 6. 7. 8. 9. lar cloning of C4 gene and identification of the class III com- plement region in the shark MHC. J Immunol 2003, 171:2461-2466. 10. Band M, Larson JH, Womack JE, Lewin HA: A radiation hybrid map of BTA23: identification of a chromosomal rearrange- ment leading to separation of the cattle MHC class II subre- gions. Genomics 1998, 53:269-275. 11. Bingulac-Popovic J, Figueroa F, Sato A, Talbot WS, Johnson SL, Gates M, Postlethwait JH, Klein J: Mapping of mhc class I and class II regions to different linkage groups in the zebrafish, Danio rerio. Immunogenetics 1997, 46:129-134. 12. Kuroda N, Figueroa F, O'HUigin C, Klein J: Evidence that the sep- aration of Mhc class II from class I loci in the zebrafish, Danio rerio, occurred by translocation. Immunogenetics 2002, 54:418-430. 13. Hansen JD, Strassburger P, Thorgaard GH, Young WP, Du Pasquier L: Expression, linkage, and polymorphism of MHC-related genes in rainbow trout, Oncorhynchus mykiss. J Immunol 1999, 163:774-786. 14. Sato A, Figueroa F, Murray BW, Malaga-Trillo E, Zaleska-Rutczynska Z, Sultmann H, Toyosawa S, Wedekind C, Steck N, Klein J: Nonlink- age of major histocompatibility complex class I and class II loci in bony fishes. Immunogenetics 2000, 51:108-116. 15. Michalova V, Murray BW, Sultmann H, Klein J: A contig map of the Mhc class I genomic region in the zebrafish reveals ancient synteny. J Immunol 2000, 164:5296-5305. 16. Sultmann H, Sato A, Murray BW, Takezaki N, Geisler R, Rauch GJ, Klein J: Conservation of Mhc class III region synteny between zebrafish and human as determined by radiation hybrid mapping. J Immunol 2000, 165:6984-6993. 17. Kasahara M: Genome dynamics of the major histocompatibil- ity complex: insights from genome paralogy. Immunogenetics 1999, 50:134-145. 18. Horton R, Wilming L, Rand V, Lovering RC, Bruford EA, Khodiyar VK, Lush MJ, Povey S, Talbot CCJ, Wright MW, Wain HM, Trowsdale J, Ziegler A, Beck S: Gene map of the extended human MHC. Nat Rev Genet 2004, 5:889-899. 19. Nei M, Gu X, Sitnikova T: Evolution by the birth-and-death process in multigene families of the vertebrate immune sys- tem. Proc Natl Acad Sci U S A 1997, 94:7799-7806. 20. 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 interme- dius) showing an unusual conservation of the peptide binding domains. J Immunol 2002, 169:1936-1947. 21. Graser R, Vincek V, Takami K, Klein J: Analysis of zebrafish Mhc using BAC clones. Immunogenetics 1998, 47:318-325. 22. Sultmann H, Mayer WE, Figueroa F, O'Huigin C, Klein J: Organiza- tion of Mhc class II B genes in the zebrafish (Brachydanio rerio). Genomics 1994, 23:1-14. 23. Phillips RB, Zimmerman A, Noakes MA, Palti Y, Morasch MR, Eiben L, Ristow SS, Thorgaard GH, Hansen JD: Physical and genetic map- ping of the rainbow trout major histocompatibility regions: evidence for duplication of the class I region. Immunogenetics 2003, 55:561-569. 24. Sambrook JG, Russell R, Umrania Y, Edwards YJ, Campbell RD, Elgar G, Clark MS: Fugu orthologues of human major histocompat- ibility complex genes: a genome survey. Immunogenetics 2002, 54:367-380. 25. Klein J, Sato A: Birth of the major histocompatibility complex. Scand J Immunol 1998, 47:199-209. 26. Seeger A, Mayer WE, Klein J: A complement factor B-like cDNA clone from the zebrafish (Brachydanio rerio). Mol Immunol 1996, 33:511-520. 27. Nonaka M, Takahashi M, Sasaki M: Molecular cloning of a lamprey homologue of the mammalian MHC class III gene, comple- ment factor B. J Immunol 1994, 152:2263-2269. 28. Kuroda N, Wada H, Naruse K, Simada A, Shima A, Sasaki M, Nonaka M: Molecular cloning and linkage analysis of the Japanese medaka fish complement Bf/C2 gene. Immunogenetics 1996, 44:459-467. 29. Gongora R, Figueroa F, Klein J: Independent duplications of Bf and C3 complement genes in the zebrafish. Scand J Immunol 1998, 48:651-658. 30. Yamashita M, Hirayoshi K, Nagata K: Characterization of multi- ple members of the HSP70 family in platyfish culture cells: Page 9 of 10 (page number not for citation purposes)