Fig. 1. Comparison of amino acid sequences corresponding with new and previously reported MHC1 U genes. The sequences of two novel MHC1 U genes, una and uoa, are quite similar to previously reported MHC1 U genes. Red asterisks indicate amino acids of peptide-anchoring residues. Black bars represent alpha1, 2, and 3 domains and transmembrane (TM) structures based on the mhc1 uba sequence. The amino acid sequences differing between WIK-derived and previously reported MHC1 U are designated with colors.

Fig. 2. Phylogenetic tree of all MHC1 U genes. The phylogenetic tree based on amino acid sequences revealed that each lineage clusters in separate branches, indicating that novel genes, una and uoa, are clustered with the MHC1 U lineage.

Fig. 3. cDNA alignment of psmb8a, daxx, and tapbp genes in reported and WIK strains. cDNA alignment of psmb8a (a), daxx (b), and tapbp (c) genes. The sequences of these genes in the WIK strain showed considerable differences from previously reported sequences of different haplotypes. The nucleotide sequences differing between WIK-derived and previously reported genes are designated with colors. GenBank accession numbers for the previously reported genes are: daxx, NM_001044949; psmb8a, NM_131392; tapbp1, NM_130974; and tapbp2, BC163081. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4. Gene structure of haplotypes. (A) Gene structure of haplotype G. Haplotype G characterized herein has similar gene order as haplotype B. The mhc1 una and uoa genes are located between daxx and psmb8a. We found only one tapbp gene on this haplotype in this region. (B) Comparison of gene structure of previously reported haplotypes (A, B, and D) and haplotype G. Note that the order of haplotypes is A, B, G, and D from top to bottom. Blue arrows indicate the genes that are highly conserved with genes on haplotype B. Red arrows indicate the genes that are divergent from genes on haplotype B. Blue shadings indicate that the gene order is conserved with haplotype B. Red shadings indicate that the gene order is divergent from haplotype B. Dotted lines in haplotype G indicate the regions not sequenced. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5. Characterization of una and uoa genes. (a) Both una and uoa genes are present in the WIK strain, whereas they are not detected in the genomes of multiple individuals of the SAT and Tubingen (TU) strains. (b) Their expression coincides with those of non-classical MHC1 U genes (ula and uma) in the WIK strain. (c) Comparison of the expression levels between uoa splice variants in the WIK strain. All four individuals show considerable differences in expression levels. Uoa-001 (longer variants) have significantly higher expression than the shorter variants.

Fig. 6. Relative expression levels of all MHC1 genes in the four individuals of the WIK strain. Relative expression levels of all MHC1 genes in gills (G), intestine (I), and kidneys (K) of the four individuals. The expression levels of each gene depend on the tissues and individuals. Although most genes are ubiquitously expressed in the gills of all individuals, the expression levels of most genes in other tissues are highly variable.