Primate MHC class I from Genomes

The major histocompatibility complex (MHC) molecule plays a central role in the adaptive immunity of jawed vertebrates. Allelic variations have been studied extensively in some primate species, however a comprehensive description of the number of genes remains incomplete. Here, a bioinformatics program was developed to identify three MHC Class I exons (EX2, EX3 and EX4) from Whole Genome Sequencing (WGS) datasets. With this algorithm, MHC Class I exons sequences were extracted from 30 WGS datasets of primates, representatives of Apes, Old World and New World monkeys and prosimians. There is a high variability in the number of genes between species. From human WGS, six viable genes (HLA-A, -B, -C, -E, -F, and -G) and four pseudogene sequences (HLA-H, -J, -L, -V) are obtained. These genes serve to identify the phylogenetic clades of MHC-I in primates. The results indicate that human clades of HLA-A -B and -C were generated shortly after the separation of Old World monkeys. The clades pertaining to HLA-E, -H and -F are found in all primate families, except in Prosimians. In the clades defined by HLA-G, -L and -J, there are sequences from Old world monkeys. Specific clades are found in the four primate families. The evolution of these genes is consistent with birth and death processes having a high turnover rates.