Table 1.
Species distribution and locus identification of 148 MHC class II cDNA sequences of wild carnivores and ungulates obtained from NCBI.
Figure 1.
Technical design of the novel HURRAH protocol for isolating MHC class II loci.
Here we show only profile reconstitution of the simplest SSCP-HD banding patterns, i.e. those representing a homozygous haplotype. For practical use, the most complicate SSCP-HD profile should also be reconstituted for comparison.
Figure 2.
Multiple sequence alignments of the amino acid sequences deduced from the full-length cDNAs.
Dots indicate identity to the first sequence and gaps represent missing amino acids. The box indicates antigen-presenting exon 2, and crosses indicate putative antigen-binding sites, as determined based on the HLA equivalents [42]. The letters and numbers following the Elda-MHC genes indicate their corresponding cDNA sequences, and the names of loci and alleles identified by the HURRAH protocol. The shaded areas indicate nucleotide differences among the Elda-MHC loci.
Figure 3.
Phylogenetic trees for the DRA, DRB, DQA, and DQB loci.
The trees were generated based on exon 3-exon 5 cDNA sequences (A, B, C, and D), intron 1 sequences (G, I, and K), intron 2 sequences (E, H, J and L), and 5′UTR-exon 1 (F). The complete intron 1 sequence of Ovar-DRA was unavailable, so we show only those based on the intron 2 sequences. The Elda-MHC genes are shaded, to allow them to be easily distinguished from the cow and sheep genes. Numbers indicate bootstrap percentages (values smaller than 50% are not shown). The numbers outside and inside the parentheses are bootstrap values for the MP and Bayesian trees, respectively. The bootstrap percentages of the NJ trees were very similar to those of the MP trees, and thus are not shown. As the branch lengths differed among trees, only the topologies are shown here. The information near each Elda-MHC gene indicates the initial cDNA sequence (a, b, c and d) and identified loci (1, 2, 3 and 4). For this analysis, the expressed HLA, BoLA and Ovar-MHC loci were identified from the relevant completely sequenced MHC class II regions of the human (HLA; NT_007592), cow (BoLA; Btau 3.1) and sheep (Ovar-MHC; EU176819).
Figure 4.
Schematic depiction of the evolution of the Elda-MHC class II genes.
For comparison, the BoLA- and Ovar-MHC genes were included. The four BoLA class II multi-locus haplotypes shown (ABCD) are based on Ballingall et al. [28], Ellis and Ballingall [29], and the Bos taurus genome sequencing project (NCBI Btau 3.1). The Ovar-MHC class II multi-locus haplotype shown was revised according to Herrmann-Hoesing et al. [10]. Recombination events are shown by the dashed-line marked conversion of two adjacent rectangles, which represent intron 1 (left) and intron 2 (right). The colors show corresponding relationships among the MHC class II loci in the three ruminants. Dotted rectangles indicate historical existence of inferred genes. UND indicates “undetected.” We also show a powerful ancestral Elda-MHC class II haplotype (F) containing all of the identified loci.
Table 2.
Comparison of the number of MHC class II loci expressed among different mammals.