Emergence and Evolution of Inter-specific Segregating Retrocopies in Cynomolgus Monkey (Macaca Fascicularis) and Rhesus Macaque (Macaca Mulatta)

Overview

Journal Sci Rep

Specialty Science

Date 2016 Sep 8

PMID 27600022

Citations 1

Authors

Xu Zhang

Qu Zhang

Bing Su

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Protein-Coding Genes' Retrocopies and Their Functions.

Kubiak M, Makalowska I Viruses. 2017; 9(4).

PMID: 28406439 PMC: 5408686. DOI: 10.3390/v9040080.

References

Goncalves I, Duret L, Mouchiroud D . Nature and structure of human genes that generate retropseudogenes. Genome Res. 2000; 10(5):672-8. PMC: 310883. DOI: 10.1101/gr.10.5.672. View

Fan Z, Zhao G, Li P, Osada N, Xing J, Yi Y . Whole-genome sequencing of tibetan macaque (Macaca Thibetana) provides new insight into the macaque evolutionary history. Mol Biol Evol. 2014; 31(6):1475-89. PMC: 4032132. DOI: 10.1093/molbev/msu104. View

Li H, Durbin R . Inference of human population history from individual whole-genome sequences. Nature. 2011; 475(7357):493-6. PMC: 3154645. DOI: 10.1038/nature10231. View

Dos Reis M, Inoue J, Hasegawa M, Asher R, Donoghue P, Yang Z . Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc Biol Sci. 2012; 279(1742):3491-500. PMC: 3396900. DOI: 10.1098/rspb.2012.0683. View

Feng Q, Moran J, Kazazian Jr H, Boeke J . Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell. 1996; 87(5):905-16. DOI: 10.1016/s0092-8674(00)81997-2. View

Esnault C, Maestre J, Heidmann T . Human LINE retrotransposons generate processed pseudogenes. Nat Genet. 2000; 24(4):363-7. DOI: 10.1038/74184. View

Li B, Dewey C . RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011; 12:323. PMC: 3163565. DOI: 10.1186/1471-2105-12-323. View

Yu Z, Morais D, Ivanga M, Harrison P . Analysis of the role of retrotransposition in gene evolution in vertebrates. BMC Bioinformatics. 2007; 8:308. PMC: 2048973. DOI: 10.1186/1471-2105-8-308. View

Emerson J, Kaessmann H, Betran E, Long M . Extensive gene traffic on the mammalian X chromosome. Science. 2004; 303(5657):537-40. DOI: 10.1126/science.1090042. View

10.

Stephens M, Donnelly P . A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet. 2003; 73(5):1162-9. PMC: 1180495. DOI: 10.1086/379378. View

11.

Hedrick P . Population genetics of malaria resistance in humans. Heredity (Edinb). 2011; 107(4):283-304. PMC: 3182497. DOI: 10.1038/hdy.2011.16. View

12.

Kaessmann H, Vinckenbosch N, Long M . RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet. 2008; 10(1):19-31. PMC: 3690669. DOI: 10.1038/nrg2487. View

13.

Wen Y, Zheng L, Liao J, Wang M, Wei Y, Guo X . Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei. Proc Natl Acad Sci U S A. 2011; 108(20):8345-50. PMC: 3100955. DOI: 10.1073/pnas.1103894108. View

14.

Zhang Q, Su B . Evolutionary origin and human-specific expansion of a cancer/testis antigen gene family. Mol Biol Evol. 2014; 31(9):2365-75. DOI: 10.1093/molbev/msu188. View

15.

Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D . Circos: an information aesthetic for comparative genomics. Genome Res. 2009; 19(9):1639-45. PMC: 2752132. DOI: 10.1101/gr.092759.109. View

16.

Mendez F, Watkins J, Hammer M . A haplotype at STAT2 Introgressed from neanderthals and serves as a candidate of positive selection in Papua New Guinea. Am J Hum Genet. 2012; 91(2):265-74. PMC: 3415544. DOI: 10.1016/j.ajhg.2012.06.015. View

17.

Hernandez R, Hubisz M, Wheeler D, Smith D, Ferguson B, Rogers J . Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science. 2007; 316(5822):240-3. DOI: 10.1126/science.1140462. View

18.

Kabza M, Kubiak M, Danek A, Rosikiewicz W, Deorowicz S, Polanski A . Inter-population Differences in Retrogene Loss and Expression in Humans. PLoS Genet. 2015; 11(10):e1005579. PMC: 4608704. DOI: 10.1371/journal.pgen.1005579. View

19.

Vinckenbosch N, Dupanloup I, Kaessmann H . Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci U S A. 2006; 103(9):3220-5. PMC: 1413932. DOI: 10.1073/pnas.0511307103. View

20.

Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y . Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature. 2008; 453(7194):539-43. DOI: 10.1038/nature06908. View