V genes in primates from whole genome sequencing data

The adaptive immune system uses V genes for antigen recognition. However, the evolutionary diversification and selection processes within and across species and orders remain poorly understood. Here, we studied the amino acid (AA) sequences obtained from the translated in-frame V exons of immunoglobulins (IG) and T cell receptors (TR) from 16 primate species whose genomes have been sequenced. Multi-species comparative analysis supports the hypothesis that V genes in the IG loci undergo birth/death processes, thereby permitting rapid adaptability over evolutionary time. We also show that multiple cladistic groupings exist in the TRA (35 clades) and TRB (25 clades) V gene loci and that each primate species typically contributes at least one V gene to each of these clades. The results demonstrate that IG V genes and TR V genes have quite different evolutionary pathways; multiple duplications can explain the IG loci results, while coevolutionary pressures can explain the phylogenetic results of the TR V gene loci. Our results suggest that there exist evolutionary relationships between V gene clades in the TRA and TRB loci. Due to the long-standing preservation of these clades, such genes may have specific and necessary roles for the viability of a species.