Figure 1.
Genomic structure and content of giant panda MHC class II region.
Boxes represent pseudogenes and the symbol “*” denotes pseudogenes that resulted from relatively recent mutation of functional genes.
Figure 2.
Phylogenetic relationships among the seven species sampled (modified from the phylogenetic tree of Springer et al. [33]).
Figure 3.
Dot plots of genomic MHC class II regions from seven species (A) and from the giant panda (B).
The plots in A and B were produced by LBDot and Pipmaker, respectively.
Figure 4.
A VISTA plot of genomic comparisons for the seven species sampled.
Boxes represent pseudogenes and the symbol “*”denotes pseudogenes that resulted from relatively recent mutation of functional genes. The color codes are as described in Figure 1.
Table 1.
Comparisons among different subregions of the MHC class II regions from the seven species sampled. The numbers mean the length of genomic DNA.
Figure 5.
Molecular timescale (in millions of years) for the phylogenetic tree based on exons 3–4 of alpha and beta genes from marsupials (in gray) and placental mammals (in black).
The Aime-DRB2 was included in the tree because of its critical position in the VISTA plot and the fact that its coding regions were relatively intact. The DMA and DMB genes were used as outgroups in constructing trees (data not shown). Triangles and rectangles represent gene clusters and lost genes, respectively; dashed and dotted lines represent the marsupial-placental and intra-Boreoeutheria divergences, respectively.
Figure 6.
Phylogenetic trees based on all exons of alpha and beta genes from marsupials and placental mammals.
The Aime-DRB2 was included in the tree because of its critical position in the VISTA plot and the fact that its coding regions were relatively intact. The DMA and DMB genes were used as outgroups in constructing trees (data not shown). Black triangles represent predicted evolutionary branches that are different from those in Figure 5.
Figure 7.
Hypothetical scenario for the birth and death of giant panda MHC class II genes.
A, B', B, C, D, E depict the ancestral MHC structure of Theria, opossum, Boreoeutheria, Laurasiatheria, Carnivora and giant panda, respectively. The opossum MHC structure was modified from Belov et al. [29]. * denotes genes that are pseudo in Euarchontoglires and ** shows those genes that are functional in ruminants. The black and gray rectangles represent respectively functional and pseudogenes in the opossum and giant panda. The colour boxes and arrows indicate ancestral MHC genes and their orientation. The dotted colour and blank symbols reflect that the ancestral genes become pseudo genes and absent ones, respectively.
Table 2.
Comparisons among different repetitive elements in MHC class II regions from the seven species sampled.