The evolutionary dynamics of autonomous non-LTR retrotransposons in the lizard anolis carolinensis shows more similarity to fish than mammals

Molecular Biology and Evolution

Volumn 26, Issue 8, 2009, Pages 1811-1822

  Novick, Peter A ^a,b   Basta, Holly ^c   Floumanhaft, Mark ^a   McClure, Marcella A ^c   Boissinot, Stéphane ^a,b  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

^c MONTANA STATE UNIVERSITY   (United States)

Author keywords

Anolis carolinensis; Long interspersed nuclear element; Retroposon; Retrotransposon

Indexed keywords

DNA; RNA;

ARTICLE; FISH; GENOME; LIZARD; LONG INTERSPERSED NUCLEAR ELEMENT; LONG TERMINAL REPEAT; MAMMAL; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; RETROPOSON; SPECIES COMPARISON;

ANIMALS; EVOLUTION, MOLECULAR; FISHES; GENOME; LIZARDS; MAMMALS; PHYLOGENY; RETROELEMENTS;

ANOLIS; ANOLIS CAROLINENSIS; MAMMALIA; REPTILIA; SQUAMATA; TELEOST FISH; VERTEBRATA;

EID: 67749095911     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp090     Document Type: Article

References (58)

1. Abrusan G, Krambeck HJ, Junier T, Giordano J, Warburton PE. 2008. Biased distributions and decay of long interspersed nuclear elements in the chicken genome. Genetics. 178:573-581.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.
3. Basta HA, Buzak AJ, McClure MA. 2007. Identification of novel retroid agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis. Evol Bioinform. 3:179-195.
4. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. 2006. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 441:87-90.
5. Ben-Aroya S, Mieczkowski PA, Petes TD, Kupiec M. 2004. The compact chromatin structure of a Ty repeated sequence suppresses recombination hotspot activity in Saccharomyces cerevisiae. Mol Cell. 15:221-231.
6. Boissinot S, Chevret P, Furano AV. 2000. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol Biol Evol. 17:915-928.
7. Boissinot S, Davis J, Entezam A, Petrov D, Furano AV. 2006. Fitness cost of LINE-1 (L1) activity in humans. Proc Natl Acad Sci USA. 103:9590-9594.
8. Boissinot S, Entezam A, Furano AV. 2001. Selection against deleterious LINE-1-containing loci in the human lineage. Mol Biol Evol. 18:926-935.
9. Burke WD, Malik HS, Jones JP, Eickbush TH. 1999. The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods. Mol Biol Evol. 16: 502-511.
10. Charlesworth B, Charlesworth D. 1983. The population dynamics of transposable elements. Genet Res. 42:1-27.
11. Charlesworth B, Langley CH. 1989. The population genetics of Drosophila transposable elements. Annu Rev Genet. 23:251-287.
12. Cooper DM, Schimenti KJ, Schimenti JC. 1998. Factors affecting ectopic gene conversion in mice. Mam Genome. 9: 355-360.
13. Cost GJ, Feng Q, Jacquier A, Boeke JD. 2002. Human L1 element target-primed reverse transcription in vitro. EMBO J. 21:5899-5910.
14. Dewannieux M, Esnault C, Heidmann T. 2003. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet. 35:41-48.
15. Dewannieux M, Heidmann T. 2005. L1-mediated retrotranspo-sition of murine B1 and B2 SINEs recapitulated in cultured cells. J Mol Biol. 349:241-247.
16. Duvernell DD, Pryor SR, Adams SM. 2004. Teleost fish genomes contain a diverse array of L1 retrotransposon lineages that exhibit a low copy number and high rate of turnover. J Mol Evol. 59:298-308.
17. Eickbush TH, Furano AV. 2002. Fruit flies and humans respond differently to retrotransposons. Curr Opin Genet Dev. 12:669-674.
18. Feng Q, Moran JV, Kazazian HH Jr., Boeke JD. 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell. 87:905-916.
19. Furano AV. 2000. The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons. Prog Nucleic Acid Res Mol Biol. 64:255-294.
20. Furano AV, Duvernell DD, Boissinot S. 2004. L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish. Trends Genet. 20:9-14.
21. Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, Jurka J. 2007. Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res. 17:992-1004.
22. Gilbert N, Labuda D. 2000. Evolutionary inventions and continuity of CORE-SINEs in mammals. J Mol Biol. 298:365-377.
23. Gish W. 1996-2004. WU-BLAST. Available from: http:// blast.wustl.edu/ (accessed May 18, 2009).
24. Guindon S, Lethiec F, Duroux P, Gascuel O. 2005. PHYML online - a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 33:W557-W559.
25. Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucleic Acids Symp Ser. 41:95-98.
26. Hull R. 2001. Classifying reverse transcribing elements: a proposal and a challenge to the ICTV. International Committee on Taxonomy of Viruses. Arch Virol. 146:2255-2261.
27. Karolchik D, Baertsch R, Diekhans M, et al. (12 co-authors). 2003. The UCSC genome browser database. Nucleic Acids Res. 31:51-54.
28. Khan H, Smit A, Boissinot S. 2006. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res. 16:78-87.
29. Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA. 1992. Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science. 256:1783-1790.
30. Kordis D, Lovsin N, Gubensek F. 2006. Phylogenomic analysis of the L1 retrotransposons in Deuterostomia. Syst Biol. 55:886-901.
31. Lander ESLM, Linton B, Birren C, et al. (254 co-authors). 2001. Initial sequencing and analysis of the human genome. Nature. 409:860-921.
32. Langley CH, Montgomery E, Hudson R, Kaplan N, Charlesworth B. 1988. On the role of unequal exchange in the containment of transposable element copy number. Genet Res. 52:223-235.
33. Luan DD, Eickbush TH. 1995. RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol Cell Biol. 15:3882-3891.
34. Luan DD, Korman MH, Jakubczak JL, Eickbush TH. 1993. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell. 72:595-605.
35. Makalowski W. 2000. Genomic scrap yard: how genomes utilize all that junk. Gene. 259:61-67.
36. Malik HS, Burke WD, Eickbush TH. 1999. The age and evolution of non-LTR retrotransposable elements. Mol Biol Evol. 16:793-805.
37. Marchler-Bauer A, Anderson JB, Derbyshire MK, et al. (25 coauthors). 2007. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 35:D237-D240.
38. Martin F, Maranon C, Olivares M, Alonso C, Lopez MC. 1995. Characterization of a non-long terminal repeat retrotransposon cDNA (L1Tc) from Trypanosoma cruzi: homology of the first ORF with the ape family of DNA repair enzymes. J Mol Biol. 247:49-59.
39. McClure MA. 1991. Evolution of retroposons by acquisition or deletion of retrovirus-like genes. Mol Biol Evol. 8:835-856.
40. McClure MA, Johnson MS, Feng DF, Doolittle RF. 1988. Sequence comparisons of retroviral proteins: relative rates of change and general phylogeny. Proc Natl Acad Sci USA. 85:2469-2473.
41. McClure MA, Richardson HS, Clinton RA, Hepp CM, Crowther BA, Donaldson EF. 2005. Automated characterization of potentially active retroid agents in the human genome. Genomics. 85:512-523.
42. Mikkelsen TS, Wakefield MJ, Aken B, et al. (62 co-authors). 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 447:167-177.
43. Neafsey DE, Blumenstiel JP, Hartl DL. 2004. Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies. Mol Biol Evol. 21:2310-2318.
44. Nekrutenko A, Li WH. 2001. Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 17:619-621.
45. Pascale E, Liu C, Valle E, Usdin K, Furano AV. 1993. The evolution of long interspersed repeated DNA (L1, LINE 1) as revealed by the analysis of an ancient rodent L1 DNA family. J Mol Evol. 36:9-20.
46. Rice P, Longden I, Bleasby A. 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16:276-277.
47. Shedlock AM, Botka CW, Zhao S, Shetty J, Zhang T, Liu JS, Deschavanne PJ, Edwards SV. 2007. Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome. Proc Natl Acad Sci USA. 104:2767-2772.
48. Skowronski J, Fanning TG, Singer MF. 1988. Unit-length line-1 transcripts in human teratocarcinoma cells. Mol Cell Biol. 8:1385-1397.
49. Smit AFA, Hubley R, Green P. 2004. RepeatMasker Open-3.0. Institute of Systems Biology. Available from: http://repeat-masker.org/ (accessed May 18, 2009).
50. Song M, Boissinot S. 2007. Selection against LINE-1 retrotransposons results principally from their ability to mediate ectopic recombination. Gene. 390:206-213.
51. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 24:1596-1599.
52. Volff JN, Bouneau L, Ozouf-Costaz C, Fischer C. 2003. Diversity of retrotransposable elements in compact pufferfish genomes. Trends Genet. 19:674-678.
53. Volff JN, Korting C, Schartl M. 2000. Multiple lineages of the non-LTR retrotransposon Rex1 with varying success in invading fish genomes. Mol Biol Evol. 17:1673-1684.
54. Voliva CF, Jahn CL, Comer MB, Hutchison CA 3rd, Edgell MH. 1983. The L1Md long interspersed repeat family in the mouse: almost all examples are truncated at one end. Nucleic Acids Res. 11:8847-8859.
55. Warren WC, Hillier LW, Marshall Graves JA, et al. (104 coauthors). 2008. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 453:175-183.
56. Waterston RH, Lindblad-Toh K, Birney E, et al. (222 co-authors). 2002. Initial sequencing and comparative analysis of the mouse genome. Nature. 420:520-562.
57. Xia X, Xie Z. 2001. DAMBE: software package for data analysis in molecular biology and evolution. J Hered. 92:371-373.
58. Zupunski V, Gubensek F, Kordis D. 2001. Evolutionary dynamics and evolutionary history in the RTE clade of non-LTR retrotransposons. Mol Biol Evol. 18:1849-1863.