BMC Genomics 2005, 6:152 http://www.biomedcentral.com/1471-2164/6/152 Table 2: List of human MHC class II and extended class II (xII) region genes used against the zebrafish whole-genome assembly. Genes with the suffix "like" are either gene fragments and/or highly similar to their human counterparts. Genes not identified by sequence similarity searches are marked as not found (NF). The official gene nomenclature for zebrafish is shown in brackets. MHC CLASS II REGION GENES HUMAN ZEBRAFISH II II II II II II II II xII xII xII xII xII xII xII xII xII xII xII xII xII xII xII xII name C6orf10 BTNL2 HLA-D* TAP2 PSMB8 TAP1 PSMB9 BRD2 COL11A2 RXRB SLC39A7 HSD17B8 RING1 VPS52 RPS18 B3GALT4 C6orf11 HKE2 RGL2 TAPBP ZNF297 DAXX LYPLA2L KIFC1 accession NM_006781 NM_019602 NM_018833 NM_004159 NM_000593 NM_002800 NM_005104 NM_080679 NM_021976 NM_006979 NM_014234 NM_002931 NM_022553 NM_022551 NM_003782 NM_005452 NM_014260 NM_004761 NM_003190 NM_005453 NM_001350 CAB63783 NM_002263 location NF NF 8 [mhc2dab] 5 [mhc2-like] 20 [mhc2-like] 19 [abcb3] 19 [psmb8] 2 [psmb5] 9 [tap1] 19 [psmb8] 2 [psmb5] 19 [brd2] 14 [brd8] 19 [col11a2] 17 [rxrb] 9 [rxrg] 19 [ke4] 19 [fabgl] NF 19 [vps52] NA303 [rps18] NF s_2182 [bing4] 14 [zgc:66282] 23 [rgl2] 19 [tpsn] 19 [znf297] 19 [daxx] 19 [lypla2l-like] 19 [kifc1] location location location 8 [mhc2daa] 19 [mhc2dcb-rs] NA14232 [mhc2dbb] NA6696 [mhc2ddb] 15 [mhc2-like] 19 [abcb3l1] 19 [abcb3l2] 19 [psmb10] 19 [psmb11] s_1793 [psmb7] 19 [psmb10] s_1793 [psmb7] 9 [brd2-like] 14 [brdt-like] 24 [col11a1] NA16779 [rxrb] 2 [rnf2] 19 [psmb11] s_549 [brd3] s_277 [brd4] 21 [rxra] s_2399 [mhc2dfb] NA6696 [mhc2-like] 19 [psmb9a] 19 [psmb9a] 5 [zgc:77289] 5 [rxra] 22 [zgc:76904] s_1722 [b3galt1] NA8827 [zgc:66282] NA14862 [rgl2-like] NA7773 [zgc:77299] NA12682 [ralgds] human genome contains at least three regions that are paralogous to the MHC [17]. These are thought to be the result of two rounds of duplications that occurred early during vertebrate evolution. In this study, we examine the genome-wide distribution of paralogous genes in zebrafish. Results and Discussion Analysis of the MHC class I region in zebrafish The MHC class I region in human embodies gene clusters coding for HLA class I molecules, histones, solute carriers, vomeronasal receptors, olfactory receptors and zinc fin- gers [18]. These clusters have undergone a large-scale expansion and each has paralogues throughout the genome. Ten representative members of the extended class I region, which are expressed and have paralogues in the human genome, and more than 30 genes that reside in the classical class I region were chosen for this analysis (Table 1). Genes that were excluded from this study included pseudogenes, zinc fingers with the tripartite motif (TRIM), and RING finger proteins. Approximately half of the human genes were identified in the zebrafish whole-genome assembly, predominantly on chromo- some 19. Because multigene families evolve by a birth- and-death process [19], orthologous genes are usually dif- ficult to identify through sequence similarity searches. Chromosome 19 harbours the largest number of MHC genes in zebrafish (Figure 1). The core region, comprising genes encoding the classical peptide presenting class I molecules (mhc1uea, mhc1uaa, mhc1ufa, mhc1uda), pro- teasome subunits (psmb8, psmb9a, psmb11, psmb10), ATP- binding cassettes (abcb3, abcb3l1, abcb3l2) and tapasin (tpsn), cluster tightly together and span approximately Page 4 of 10 (page number not for citation purposes)