BMC Genomics 2005, 6:152 http://www.biomedcentral.com/1471-2164/6/152 >bat3 (-) tcf19-L C6orf27-L >agpat3 (+) >mhc1-L >mhc1-L >mhc1-L >zgc:64115 1 vars2 (-) >pbx1a (-) >tubb5 (-) >mhc2-L atf6-L 11 20 rnf2 (+) > tnw (+) > tnr psmb5 (+) 2 >agpat4 13 >rxra (-) >bf/c2 (+) 21 >hsp70 (+) >hsp70 >hsp70 3 >tubb2 (+) >brd8 (+) >zgc:66282 >brdt-L >zgc:92762 ier5 (+) >zgc:76904 >c3 (-) 14 22 4 >ddr2 >c4 >mhc2-L msh5 >a2m >gabbr1 (+) >dhx16 (+) 15 >rgl2 (-) >ck2b (-) >tubb2 23 >tnc (+) zgc:73179 (+) >mhc2-L atp6v1g1 (+) >zgc:77289 (+) >rxr(a) (+) >notch1 (+) 5 >flot1b (+) >tnx-L >ddr1-L gnl1 >ddx39 (-) >clica (-) pou5f1 (-) >col11a1 (-) 6 cyp21a2 smx5 (+) >clic4 (+) >rxrb (-) >bf/c2 rdbp >hsp70 >skiv2l 16 17 18 24 NA17761 NA17767 >hsp70 (-) >mhc2dab (+) >mhc2daa (+) 8 >zgc:77538 stk19-L (-) >pbx3b zbtb12 bat8 zgc:64108 neu1 tap1 >brd2-L >rxrg (-) 9 CORE MHC vps52 (+) >ppt2 (+) ke4 (+) ddah1 c6orf134 19 v>azgrsc2:6-L3773 zgc:77721 (+) >tnf >gabbr1 (-) >skiv2l (+) c6orf31-L >ck2b (+) bat2-L (+) >ck2b >mhc2dcb-rs >bat3-L (-) c6orf136 zgc:85667 mrps18b ppp1r10 (+) lypla2l-L daxx (+) znf297 (+) kifc1 (+) >flot1 (+) tpsn (+) >mhc1uda (+) >abcb3 (+) >mhc1ufa (+) >abcb3l2 (+) >mhc1uaa (+) >mhc1uea (+) >psmb8 (+) >psmb10 (+) >psmb11 (+) >psmb9a (+) >abcb3l1 (+) >brd2 (+) fabgl (+) col11a2 (+) FMiagpuorefm1ajor histocompatibility genes and their paralogues in zebrafish (not to scale) Map of major histocompatibility genes and their paralogues in zebrafish (not to scale). Only chromosomes and two unmapped contigs (NA17761 and NA17767) that harbour MHC-related genes are shown. Orthologues or paralogues of human MHC class I region genes are shown in red, of class II region genes in blue, and class III region genes in green. Genes with the suffix "L" for like are either gene fragments and/or highly similar to their human counterparts. Genes that have more than one copy in the genome are shown by a greater than (>) symbol. Similarities and differences between the whole-genome assembly and mapping information present in the ZFIN database are shown by plus (+) and minus (-) signs, respectively. The core MHC has been compiled from five genomic clones spanning this region [EMBL:AL672216, EMBL:AL672151, EMBL:AL672164, EMBL:AL672176]. present in trout, stickleback, common guppy and cichlid fish [13,14]. This observation demonstrates that the sepa- ration of the MHC class I and class II loci is characteristic of teleost fish, which represent half of all vertebrates. Since the genes of the immune system were present in the com- mon ancestor of tetrapods and teleosts, the differences in their genomic organisation may be the result of lineage- specific chromosomal events such as duplications, inver- sions, deletions and translocations. The genome of the zebrafish is currently being sequenced at the Wellcome Trust Sanger Institute. The availability of sequence data will allow an insight into the understand- ing and evolution of the immune system in fish. To date, small regions containing major histocompatibility genes have been mapped by radiation hybrid mapping and sequencing of select genomic clones [15,16]. With the ongoing whole-genome sequencing efforts and the com- pilation of physical maps, it is now possible to examine larger genomic regions and assess the degree of shared synteny between mammals and fish on a genome-wide scale. Here we have utilised a comprehensive whole- genome shotgun assembly data set to fully analyse the zebrafish loci that are related to the human MHC. The Page 3 of 10 (page number not for citation purposes)