Emergence and evolution of inter-specific segregating retrocopies in cynomolgus monkey (Macaca fascicularis) and rhesus macaque (Macaca mulatta).
Retroposition is an RNA-mediated mechanism to generate gene duplication, and is believed to play an important role in genome evolution and phenotypic adaptation in various species including primates. Previous studies suggested an elevated rate of recent retroposition in the rhesus macaque genome. To better understand the impact of retroposition on macaque species which have undergone an adaptive radiation approximately 3-6 million years ago, we developed a bioinformatics pipeline to identify recently derived retrocopies in cynomolgus monkeys. As a result, we identified seven experimentally validated young retrocopies, all of which are polymorphic in cynomolgus monkeys. Unexpectedly, five of them are also present in rhesus monkeys and are still segregating. Molecular evolutionary analysis indicates that the observed inter-specific polymorphism is attribute to ancestral polymorphism. Further population genetics analysis provided strong evidence of balancing selection on at least one case (Crab-eating monkey retrocopy 6, or CER6) in both species. CER6 is in adjacent with an immunoglobulin related gene and may be involved in host-pathogen interaction, a well-known target of balancing selection. Altogether, our data support that retroposition is an important force to shape genome evolution and species adaptation.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.|Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China.
Xu
X
Zhang
Department of Human Evolutionary Biology, Graduate School of Art and Science, Harvard University, Cambridge, MA 02138, USA.|Perspective Sciences, 18 Qingfeng North Road, Phoenix Building A, North New Zone, Chongqing 401320, China.
Qu
Q
Zhang
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
Bing
B
Su
D000818:Animals; D001483:Base Sequence; D020090:Chromosome Segregation / Q000235:genetics*; D019295:Computational Biology; D003198:Computer Simulation; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D063990:Gene Ontology; D005828:Genetics, Population; D016678:Genome; D016013:Likelihood Functions; D008252:Macaca fascicularis / Q000235:genetics*; D008253:Macaca mulatta / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D013045:Species Specificity
D018626:Retroelements