Next-generation Sequencing of MHC Class I Genes Reveals Trans-species Polymorphism in Eutropis multifasciata and Other Species of Scincidae

The genes of the major histocompatibility complex (MHC) encode cell surface proteins that are essential for adaptive immunity. MHC genes show the most prominent genetic diversity in vertebrates, reflecting the adaptation of populations to their evolving environment, population survival and reproduction. In the present study, we used next -generation sequencing (NGS) to study the loci polymorphism of exon 3 of the MHC class I genes in an ovoviviparous skink, the many-lined sun skink, Eutropis multifasciata and five other species of Scincidae, to quantify genetic variation. In addition, we genotyped the same MHC class I genes of E. multifasciata using clone sequencing, to directly compare the effectiveness of both analytical techniques for MHC genotyping. NGS detected 20 MHC class I alleles in E. multifasciata, and 2 to 15 alleles in the other five Scincidae species. However, clone sequencing detected only 15 of those MHC class I alleles in E. multifasciata. In addition, trans -species polymorphism of MHC class I genes was studied by constructing a phylogenetic tree using the gene sequences obtained by NGS. Phylogenetic analysis revealed that MHC class I alleles were shared among different species of Scincidae with trans-species polymorphism, and did not exhibit specific genealogical inheritance. These results have important implications for understanding polymorphism interspecies diversity in the MHC genes of Scincidae, and the evolution of the MHC more broadly.