The changing tails of a novel short interspersed element in Aedes aegypti: Genomic evidence for slippage retrotransposition and the relationship between 3′ tandem repeats and the poly(dA) tail

Genetics

Volumn 168, Issue 4, 2004, Pages 2037-2047

  Tu, Zhijian ^a   Li, Song ^a   Mao, Chunhong ^b  

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

^b VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA;

AEDES AEGYPTI; ARTICLE; GENE; GENE DELETION; GENE GECKO; GENE REPLICATION; GENE SEQUENCE; MICROSATELLITE MARKER; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RETROPOSON; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SHORT INTERSPERSED REPEAT; TANDEM REPEAT;

AEDES; ANIMALS; BASE SEQUENCE; EXPRESSED SEQUENCE TAGS; MOLECULAR SEQUENCE DATA; POLY A; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS; TANDEM REPEAT SEQUENCES;

AEDES AEGYPTI; ARACHNIDA; GEKKO; HEXAPODA;

EID: 11244303622     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.032045     Document Type: Article

References (37)

1. ADAMS, D. S., T. H. EICKBUSH, R. J. HERRERA and P. M. LIZARDI, 1986 A highly reiterated family of transcribed oligo(A)-terminated, interspersed DNA elements in the genome of Bombyx mori. J. Mol. Biol. 187: 465-478.
2. ALTSCHUL, S. F., T. L. MADDEN, A. A. SCHAFFER, J. ZHANG, Z. ZHANG et al., 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
3. ARCOT, S. S., Z. WANG, J. L. WEBER, P. L. DEININGER and M. A. BATZER, 1995 Alu repeats: a source for the genesis of primate microsatellites. Genomics 29: 136-144.
4. BENSAADI-MERCHERMEK, N., C. CAGNON, I. DESMONS, J. C. SALVADO, S. KARAMA et al., 1997 CM-gag, a transposable-like element reiterated in the genome of Culex pipiens mosquitoes, contains only a gag gene. Genetica 100: 141-148.
5. BIEDLER, J., and Z. TU, 2003 Non-LTR retrotransposons in the African malaria mosquito, Anopheles gambiae: unprecedented diversity and evidence of recent activity. Mol. Biol. Evol. 20: 1811-1825.
6. BOEKE, J. D., 2003 The unusual phylogenetic distribution of retro transposons: a hypothesis. Genome Res. 13: 1975-1983.
7. BUCHETON, A., I. BUSSEAU and D. TENINGES, 2002 I elements in Drosophila melanogaster, pp. 796-812 in Mobile DNA II, edited by N. CRAIG, R. CRAIGIE, M. GELLERT and A LAMBOWITZ. American Society for Microbiology Press, Washington, DC.
8. CHABOISSIER, M. C., D. FINNEGAN and A. BUCHETON, 2000 Retrotransposition of the I factor, a non-long terminal repeat retrotransposon of Drosophila, generates tandem repeats at the 3′ end. Nucleic Acids Res. 28: 2467-2472.
9. CHAMBEYRON, S., A. BUCHETON and I. BUSSEAU, 2002 Tandem UAA repeats at the 3′-end of the transcript are essential for the precise initiation of reverse transcription of the I factor in Drosophila melanogaster. J. Biol. Chem. 277: 17877-17882.
10. DEININGER, P. L., 1989 SINEs: short interspersed repeated DNA elements in higher eukaryotes, pp. 619-636 in Mobile DNA, edited by D. BERG and M. HOWE. American Society for Microbiology Press, Washington, DC.
11. DEWANNIEUX, M., C. ESNAULT and T. HEIDMANN, 2003 LINE-mediated retrotransposition of marked Alu sequences. Nat. Genet. 35: 41-48.
12. EICKBUSH, T. H., and H. S. MALIK, 2002 Origins and evolution of retrotransposons, pp. 1111-1144 in Mobile DNA II, edited by N. L. CRAIG, R. CRAIGIE, M. GELLERT and A. M. LAMBOWITZ. American Society for Microbiology Press, Washington, DC.
13. FAGERBERG, A. J., R. E. FULTON and W. C. BLACK, 2001 Microsatellite loci are not abundant in all arthropod genomes: analyses in the hard tick, Ixodes scapularis and the yellow fever mosquito, Aedes aegypti. Insect Mol. Biol. 10: 225-236.
14. FESCHOTTE, C., N. FOURRIER, I. DESMONS and C. MOUCHES, 2001 Birth of a retroposon: the twin SINE family from the vector mosquito Culex pipiens may have originated from a dimeric tRNA precursor. Mol. Biol. Evol. 18: 74-84.
15. FINNEGAN, D. J., 1992 Transposable elements. Curr. Opin. Genet. Dev. 2: 861-867.
16. JURKA, J., 1995 Origin and evolution of Alu repetitive elements, pp. 25-41 in The Impact of Short Interspersed Elements (SINEs) on the Host Genome, edited by R. J. MARAIA. R. G. Landes, Austin, TX.
17. JURKA, J., and C. PETHIYAGODA, 1995 Simple repetitive DNA sequences from primates: compilation and analysis. J. Mol. Evol. 40: 120-126.
18. KAJIKAWA, M., and N. OKADA, 2002 LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 111: 433-444.
19. KAPITONOV, V. V., and J. JURKA, 2003 A novel class of SINE elements derived from 5S rRNA. Mol. Biol. Evol. 20: 694-702.
20. LAI, Y., and F. SUN, 2003 The relationship between microsatellite slippage mutation rate and the number of repeat units. Mol. Biol. Evol. 20: 2123-2131.
21. LUAN, D. D., and T. H. EICKBUSH, 1995 RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Mol. Cell. Biol. 15: 3882-3891.
22. OHSHIMA, K., M. HAMADA, Y. TERAI and N. OKADA, 1996 The 3′ ends of tRNA-derived short interspersed repetitive elements are derived from the 3′ ends of long interspersed repetitive elements. Mol. Cell. Biol. 16: 3756-3764.
23. OKADA, N., 1991 SINEs. Curr. Opin. Genet. Dev. 1: 498-504.
24. OKADA, N., and M. HAMADA, 1997 The 3′ ends of tRNA-derived SINEs originated from the 3′ ends of LINEs: a new example from the bovine genome. J. Mol. Evol. 44 (Suppl. 1): S52-S56.
25. OSTERTAG, E. M., and H. H. KAZAZIAN, JR., 2001 Biology of mammalian L1 retrotransposons. Annu. Rev. Genet. 35: 501-538.
26. PETROV, D. A., Y. T. AMINETZACH, J. C. DAVIS, D. BENSASSON and A. E. HIRSH, 2003 Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila. Mol. Biol. Evol. 20: 880-892.
27. RAI, K. S., and W. C. T. BLACK, 1999 Mosquito genomes: structure, organization, and evolution. Adv. Genet. 41: 1-33.
28. SUZUKI, T., T. UEDA, T. YOKOGAWA, K. NISHIKAWA and K. WATANABE, 1994 Characterization of serine and leucine tRNAs in an asporogenic yeast Candida cylindracea and evolutionary implications of genes for tRNA(Ser)CAG responsible for translation of a non-universal genetic code. Nucleic Acids Res. 22: 115-123.
29. SWOFFORD, D. L., 2002 Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates, Sunderland, MA.
30. SZAK, S. T., O. K. PICKERAL, W. MAKALOWSKI, M. S. BOGUSKI, D. LANDSMAN et al., 2002 Molecular archeology of L1 insertions in the human genome. Genome Biol. 3: research0052.
31. THOMPSON, J. D., T. J. GIBSON, F. PLEWNIAK, F. JEANMOUGIN and D. G. HIGGINS, 1997 The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876-4882.
32. TU, Z., 1999 Genomic and evolutionary analysis of Feilai, a diverse family of highly reiterated SINEs in the yellow fever mosquito, Aedes aegypti. Mol. Biol. Evol. 16: 760-772.
33. TU, Z., 2001a Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae. Proc. Natl. Acad. Sci. USA 98: 1699-1704.
34. TU, Z.,2001b Maque, a family of extremely short interspersed repetitive elements: characterization, possible mechanism of transposition, and evolutionary implications. Gene 263: 247-253.
35. TU, Z., 2004 Insect Transposable Elements in Comprehensive Insect Physiology, Biochemistry, Pharmacology, and Molecular Biology, Elsevier, Oxford.
36. TU, Z., and J. J. HILL, 1999 MosquI, a novel family of mosquito retrotransposons distantly related to the Drosophila I factors, may consist of elements of more than one origin. Mol. Biol. Evol. 16: 1675-1686.
37. ZAR, J., 1996 Biostatistical Analysis. Prentice-Hall, Saddle River, NJ.