Conclusion
Rhesus macaques (Macaca mulatta) is the most extensively used non-human primate medical disease model. The higher genomic diversity in this species than in human render it valuable for addressing medical as well as evolutionary questions. Despite the unique advantage of holding methylation signals, nanopore long-read data has not been utilized to investigate issues related to reference and variants. Here, we provided the long reads for a Chinese macaque (CR2) and conducted SVs-oriented analyses on genomic between two subspecies. We found lower strengths of methylation but higher rates of recombination for duplications than other types of SVs (deletions, insertions, and inversions). We also revealed the selective sweep and the “faster-X effect” underlying the SVs distribution along the chromosomes. Some SVs-involved genes under selective sweep are causal genes for multiple neurodevelopmental diseases and innovative traits in human. Our study characterizes multiple molecular features and evolutionary forces underlying SVs of the rhesus macaque, which could shed light on the translational medicine from this important medical model to human per se.