**2.3.3 The MHC in monotremes**

Although the platypus genome has been sequenced, the high GC and repeat content hampered this sequencing effort, leaving the assembly with many more gaps than other mammalian genomes sequenced to a six-fold depth by Sanger sequencing (Warren et al., 2008). As a result, complete annotation of the platypus MHC as a region was impossible because MHC genes were found on many sequence contigs and/or scaffolds. However, three BAC clones were completely sequenced and mapped to platypus chromosomes (Dohm et al., 2007). One of these BACs, localized to chromosome 3, only contained a processed class I pseudogene. Of the remaining two BACs, one contained two Class I genes and two Class II genes as well as antigen processing genes, while the other contained mainly Class III genes. The most surprising result came from FISH-mapping, which revealed that platypus MHC is not contiguous and maps to the pseudoautosomal region of two pairs of sex chromsomes. The Class I and II genes were located on X3/Y3 and the Class III region on X4/Y4. Subsequent FISH-mapping of BACs containing these same genes in the echidna demonstrated that this separation of the MHC onto two different pairs of sex chromosomes was a common feature for monotremes. Monotremes are the only mammals known to date to have the MHC reside on sex chromosomes (Dohm et al., 2007).
