Burst of young retrogenes and independent retrogene formation in mammals

PLoS ONE

Volumn 4, Issue 3, 2009, Pages

  Pan, Deng ^a   Zhang, Liqing ^a,b  

^a State University   (United States)

^b VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE; GENE FUNCTION; GENOME; MAMMAL; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; MULTIGENE FAMILY; RETROGENE; RETROPOSON; RIBOSOME; ANIMAL; BIOLOGY; EVOLUTION; GENETICS; HUMAN;

MAMMALIA; PRIMATES;

ANIMALS; BIOLOGICAL EVOLUTION; COMPUTATIONAL BIOLOGY; GENOME; HUMANS; RETROELEMENTS;

EID: 63449122253     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005040     Document Type: Article

References (51)

1. Zhang J (2003) Evolution by gene duplication: an update. Trends in Ecology and Evolution 18: 292-298.
2. Brosius J (1991) Retroposons-seeds of evolution. Science 251: 753.
3. Zhang Z, Harrison P, Gerstein M (2002) Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res 12: 1466-82.
4. Torrents D, Suyama M, Zdobnov E, Bork P (2003) A genome-wide survey of human pseudogenes. Genome Res 13: 2559-67.
5. Zhang Z, Harrison PM, Liu Y, Gerstein M (2003) Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res 13: 2541-58.
6. Pavlicek A, Gentles AJ, Paces J, Paces V, Jurka J (2006) Retroposition of processed pseudogenes: the impact of RNA stability and translational control. Trends Genet 22: 69-73.
7. Kaessmann H, Vinckenbosch N, Long M (2009) RNA-based gene duplication: mechanistic and evolutionary insights. NATURE REVIEWS GENETICS 10: 19-31.
8. Robinson R (2005) Retrocopied genes may enhance male fitness. Plos biology 3: e399.
9. Betran E, Thornton K, Long M (2002) Retroposed new genes out of the X in Drosophila. Genome Res 12: 1854-9.
10. Emerson JJ, Kaessmann H, Betran E, Long M (2004) Extensive gene traffic on the mammalian X chromosome. Science 303: 537-40.
11. Marques AC, Dupanloup I, Vinckenbosch N, Reymond A, Kaessmann H (2005) Emergence of young human genes after a burst of retroposition in primates. PLoS Biol 3: e357.
12. Vinckenbosch N, Dupanloup I, Kaessmann H (2006) Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci U S A 103: 3220-5.
13. Bai Y, Casola C, Feschotte C, Betran E (2007) Comparative Genomics Reveals a Constant Rate of Origination and Convergent Acquisition of Functional Retrogenes in Drosophila. Genome Biol 8: R11.
14. Pan D, Zhang L (2007) Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates. Genome Biol 8: R158.
15. Esnault C, Maestre J, Heidmann T (2000) Human LINE retrotransposons generate processed pseudogenes. Nat Genet 24: 363-7.
16. Furano AV (2000) The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons. Prog Nucleic Acid Res Mol Biol 64: 255-94.
17. Furano AV, Duvernell DD, Boissinot S (2004) L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish. Trends Genet 20: 9-14.
18. Casavant NC, Scott L, Cantrell MA, Wiggins LE, Baker RJ, et al. (2000) The end of the LINE? : lack of recent L1 activity in a group of South American rodents. Genetics 154: 1809-17.
19. Boissinot S, Roos C, Furano AV (2004) Different rates of LINE-1 (L1) retrotransposon amplification and evolution in New World monkeys. J Mol Evol 58: 122-30.
20. Gentles AJ, Karlin S (1999) Why are human G-protein-coupled receptors predominantly intronless? Trends Genet 15: 47-9.
21. Brosius J (1999) Many G-protein-coupled receptors are encoded by retrogenes. Trends Genet 15: 304-5.
22. Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, et al. (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res 17: 669-81.
23. Ezawa K, OOta S, Saitou N (2006) Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Genome-wide search of gene conversions in duplicated genes of mouse and rat. Mol Biol Evol 23: 927-40.
24. Burch J, Davis D, Haas N (1993) Chicken repeat 1 elements contain a pol-like open reading frame and belong to the non-long terminal repeat class of retrotransposons. Proc Natl Acad Sci USA 90: 8199-8203.
25. Haas NB, Grabowski JM, North J, Moran JV, Kazazian HH, et al. (2001) Subfamilies of CR1 non-LTR retrotransposons have different 5′UTR sequences but are otherwise conserved. Gene 265: 175-83.
26. International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
27. Eickbush TH, Furano AV (2002) Fruit flies and humans respond differently to retrotransposons. Curr Opin Genet Dev 12: 669-74.
28. Volff JN, Bouneau L, Ozouf-Costaz C, Fischer C (2003) Diversity of retrotransposable elements in compact pufferfish genomes. Trends Genet 19: 674-8.
29. Crainey JL, Garvey CF, Malcolm CA (2005) The origin and evolution of mosquito APE retroposons. Mol Biol Evol 22: 2190-7.
30. Nikolaev SI, Montoya-Burgos JI, Popadin K, Parand L, Margulies EH, et al. (2007) Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 104: 20443-20448.
31. Li WH (1997) Molecular evolution. Sunderland, MA: Sinauer Associates.
32. Petrov DA, Hartl DL (1998) High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. Mol Biol Evol 15: 293-302.
33. Harrison PM, Milburn D, Zhang Z, Bertone P, Gerstein M (2003) Identification of pseudogenes in the Drosophila melanogaster genome. Nucleic Acids Res 31: 1033-7.
34. Petrov DA (2002) DNA loss and evolution of genome size in Drosophila. Genetica 115: 81-91.
35. Demuth JP, Bie TD, Stajich JE, Cristianini N, Hahn MW (2006) The evolution of Mammalian gene families. PLoS ONE 1: e85.
36. Hedges SB (2002) The origin and evolution of model organisms. Nat Rev Genet 3: 838-49.
37. Killian JK, Buckley TR, Stewart N, Munday BL, Jirtle RL (2001) Marsupials and Eutherians reunited: genetic evidence for the Theria hypothesis of mammalian evolution. Mamm Genome 12: 513-7.
38. Graves JA, Westerman M (2002) Marsupial genetics and genomics. Trends Genet 18: 517-21.
39. Wakefield MJ, Graves JA (2003) The kangaroo genome. Leaps and bounds in comparative genomics. EMBO Rep 4: 143-7.
40. Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, et al. (2002) Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298: 149-59.
41. Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, et al. (2005) BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21: 3439-40.
42. Enright AJ, Dongen SV, Ouzounis CA (2002) An efficient algorithm for largescale detection of protein families. Nucleic Acids Research 30: 1575-1584.
43. Thompson J, Higgins D, Gibson T (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
44. Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17: 32-43.
45. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-6.
46. Felsenstein J (1989) PHYLIP - Phylogeny Inference Package. Cladistics 5: 164-166.
47. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-25.
48. Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol 29: 170-9.
49. Felsenstein J, Churchill GA (1996) A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol 13: 93-104.
50. Müller J, Müller K (2004) TreeGraph: automated drawing of complex tree figures using an extensible tree description format. Molecular Ecology Notes 4: 786-788.
51. R Development Core Team (2006) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; ISBN 3-900051-07-0.