The role of mRNA-based duplication in the evolution of the primate genome

•Two burst of retropositions were found during primate evolution.•Approximately 10% intact retrocopies (potential functional genes) may be under positive selection.•Over 4% retrocopies eventually become functional after their origination.•Human intact retrocopies are enriched for functions involved in transcription. Analysis of the human genome suggests novel genes created by retroposition may play an important role in primate evolution. However, data from non-human primates is still scarce. A comprehensive comparison was thus performed among four primate genomes (human, chimpanzee, orangutan, and macaque), which detects elevated rates of retroposition in both the common ancestor of hominoids and macaques. Further analysis shows approximately 10% of intact retrocopies may be under positive selection and at least 4% of retrocopies become functional copies eventually. Moreover, human intact retrocopies were found enriched in transcription-related functions. Collectively, these findings emphasize the important contribution of retroposition to primate genome evolution.