A contig map of the Mhc class I genomic region in the zebrafish reveals ancient synteny

In contrast to the human and mouse Mhc, in which the clusters of class I an d class II loci reside in close vicinity to one another; in the zebrafish, Danio rerio, they are found in different linkage groups. Chromosome walking using BAC (bacterial artificial chromosome) and PAC (P1 artificial chromos ome) clones reveals the zebrafish class I region to occupy a segment of sim ilar to 450 kb and to encompass at least 19 loci. These include three class I (Dare-UDA, -UEA, -UFA), five proteasome subunit beta (PSMB8, -9A, -9C, - 11, -12), two TAPs (TAP2A, TAP2B), and one TAP binding protein (TAPBP), Thi s arrangement contrasts with the arrangements found in human and mouse Mhc, in which the orthologues of the PSMB, TAP, and TAPBP loci reside within th e class II region. In addition to this main zebrafish class I contig, a sho rter contig of about 150 kb contains two additional class I (UBA, UCA) and at least five other loci. It probably represents a different haplotype of p art of the class I region. The previously identified UAA gene shares an ide ntical 5' part with UEA, but the two genes differ in their 3' parts. One of them is probably the result of an unequal crossing over. The described org anization has implications for the persistence of syntenic relationships, c oevolution of loci, and interpretation of the origin of the human/mouse Mhc organization.