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Cited by 288Chromosomal and Genetic VariationsGenomic variations and chromosomal abnormalitiesGenome Rearrangement Algorithms

Molecular paleontology of transposable elements in the Drosophila melanogaster genome

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Kapitonov, Vladimir V., Jurka, Jerzy·2003·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.0732024100PMC PMC164487
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Abstract

We report here a superfamily of “cut and paste” DNA transposons called Transib . These transposons populate the Drosophila melanogaster and Anopheles gambiae genomes, use a transposase that is not similar to any known proteins, and are characterized by 5-bp target site duplications. We found that the fly genome, which was thought to be colonized by the P element <100 years ago, harbors ≈5 million year (Myr)-old fossils of ProtoP , an ancient ancestor of the P element. We also show that Hoppel , a previously reported transposable element (TE), is a nonautonomous derivate of ProtoP . We found that the “rolling-circle” Helitron transposons identified previously in plants and worms populate also insect genomes. Our results indicate that Helitron s were horizontally transferred into the fly or/and mosquito genomes. We have also identified a most abundant TE in the fly genome, DNAREP1 _ DM , which is an ≈10-Myr-old footprint of a Penelope -like retrotransposon. We estimated that TEs are three times more abundant than reported previously, making up ≈22% of the whole genome. The chromosomal and age distributions of TEs in D. melanogaster are very similar to those in Arabidopsis thaliana . Both genomes contain only relatively young TEs (<20 Myr old), constituting a main component of paracentromeric regions.

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  • Transib transposons belong to the only superfamily of eukaryotic DNA transposons with 5-bp TSDs generated upon insertions into the genome.

    “Given the predominance of 5-bp TSDs, it is striking that Transib transposons belong to the only superfamily of eukaryotic DNA transposons with 5-bp TSDs generated upon insertions into the genome [17,24].”

    From RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons (2005) · cites this paper as [17]

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  1. [2]Kidwell, M. G. & Lisch, D. R. (2001) Evol. Int. J. Org. Evol. 55, 1–24. [DOI] [PubMed] [Google Scholar]
  2. [3]Fedoroff, N. V. (1999) Ann. N.Y. Acad. Sci. 870, 251–264. [DOI] [PubMed] [Google Scholar]
  3. [4]Craig, N. L. (1995) Science 270, 253–254. [DOI] [PubMed] [Google Scholar]
  4. [5]Adams, M. D., Celniker, S. E., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F., et al. (2000) Science 287, 2185–2195. [DOI] [PubMed] [Google Scholar]
  5. [6]Kapitonov, V. V. & Jurka, J. (1999) Genetica 107, 27–37. [PubMed] [Google Scholar]
  6. [7]Kapitonov, V. V. & Jurka, J. (2001) Proc. Natl. Acad. Sci. USA 98, 8714–8719. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. [8]Pimpinelli, S., Berloco, M., Fanti, L., Dimitri, P., Bonaccorsi, S., Marchetti, E., Caizzi, R., Caggese, C. & Gatti, M. (1995) Proc. Natl. Acad. Sci. USA 92, 3804–3808. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. [9]Kapitonov, V. V., Holmquist, G. P. & Jurka, J. (1998) Mol. Biol. Evol. 15, 611–612. [DOI] [PubMed] [Google Scholar]
  9. [10]Ananiev, E. V., Phillips, R. L. & Rines, H. W. (1998) Proc. Natl. Acad. Sci. USA 95, 10785–10790. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. [11]The Arabidopsis Genome Initiative (2000) Nature 408, 796–815. [DOI] [PubMed] [Google Scholar]
  11. [12]Jurka, J. (2000) Trends Genet. 16, 418–420. [DOI] [PubMed] [Google Scholar]
  12. [13]Jurka, J., Klonowski, P., Dagman, V. & Pelton, P. (1996) Comput. Chem. 20, 119–121. [DOI] [PubMed] [Google Scholar]
  13. [14]Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990) J. Mol. Biol. 215, 403–410. [DOI] [PubMed] [Google Scholar]
  14. [15]Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389–3402. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. [16]Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673–4680. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. [17]Nicholas, K. B., Nicholas, H. B. & Deerfield, D. W. (1997) EMBNET News 4, 1–4. [Google Scholar]
  17. [18]Salamov, A. A. & Solovyev, V. V. (2000) Genome Res. 10, 516–522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. [19]Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001) Bioinformatics 17, 1244–1245. [DOI] [PubMed] [Google Scholar]
  19. [21]Bernstein, M., Lersch, R. A., Subrahmanyan, L. & Cline, T. W. (1995) Genetics 139, 631–648. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. [22]Holt, R. A., Subramanian, G. M., Halpern, A., Sutton, G. G., Charlab, R., Nusskern, D. R., Wincker, P., Clark, A. G., Ribeiro, J. M., Wides, R., et al. (2002) Science 298, 129–149.12364791 [Google Scholar]
  21. [23]Kurenova, E. V., Leibovich, B. A., Bass, I. A., Bebikhov, D. V., Pavlova, M. N. & Danilevskaia, O. N. (1990) Genetika 26, 1701–1712. [PubMed] [Google Scholar]
  22. [24]Kholodilov, N. G., Bolshakov, V. N., Blinov, V. M., Solovyov, V. V. & Zhimulev, I. F. (1988) Chromosoma 97, 247–253. [DOI] [PubMed] [Google Scholar]
  23. [25]Bartolome, C., Maside, X. & Charlesworth, B. (2002) Mol. Biol. Evol. 19, 926–937. [DOI] [PubMed] [Google Scholar]
  24. [26]Clark, J. B. & Kidwell, M. G. (1997) Proc. Natl. Acad. Sci. USA 94, 11428–11433. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. [27]Hagemann, S. & Pinsker, W. (2001) Mol. Biol. Evol. 18, 1979–1982. [DOI] [PubMed] [Google Scholar]
  26. [28]Reiss, D. E., Quesneville, H., Noaud, D., Andrieu, O. & Anxolabehere, D. (2003) Mol. Biol. Evol. 20, 869–879. [DOI] [PubMed] [Google Scholar]
  27. [29]Feschotte, C. & Wessler, S. R. (2002) Proc. Natl. Acad. Sci. USA 99, 280–285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. [30]Gaunt, M. W. & Miles, M. A. (2002) Mol. Biol. Evol. 19, 748–761. [DOI] [PubMed] [Google Scholar]
  29. [31]Sharakhov, I. V., Serazin, A. C., Grushko, O. G., Dana, A., Lobo, N., Hillenmeyer, M. E., Westerman, R., Romero-Severson, J., Costantini, C., Sagnon, N., et al. (2002) Science 298, 182–185. [DOI] [PubMed] [Google Scholar]
  30. [32]Zdobnov, E. M., von Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R. R., Christophides, G. K., Thomasova, D., Holt, R. A., Subramanian, G. M., et al. (2002) Science 298, 149–159. [DOI] [PubMed] [Google Scholar]
  31. [33]Fraser, M. J., Ciszczon, T., Elick, T. & Bauser, C. (1996) Insect Mol. Biol. 5, 141–151. [DOI] [PubMed] [Google Scholar]
  32. [34]Cary, L. C., Goebel, M., Corsaro, B. G., Wang, H. G., Rosen, E. & Fraser, M. J. (1989) Virology 172, 156–169. [DOI] [PubMed] [Google Scholar]
  33. [35]Smit, A. F. A. (2002) Repbase Rep. 2 (1), 35. [Google Scholar]
  34. [36]Kapitonov, V. V. & Jurka, J. (2002) Repbase Rep. 2 (6), 21. [Google Scholar]
  35. [37]Evgen'ev, M. B., Zelentsova, E. S., Shostak, N. G., Kozitsina, M., Barskyi, V., Lankenau, D. H. & Corces, V. G. (1997) Proc. Natl. Acad. Sci. USA 94, 196–201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. [38]Pyatkov, K. I., Shostak, N. G., Zelentsova, E. S., Lyozin, G. T., Melekhin, M. I., Finnegan, D. J., Kidwell, M. G. & Evgen'ev, M. B. (2002) Proc. Natl. Acad. Sci. USA 99, 16150–16155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. [40]Smit, A. F. (1999) Curr. Opin. Genet. Dev. 9, 657–663. [DOI] [PubMed] [Google Scholar]
  38. [41]Pantazidis, A., Labrador, M. & Fontdevila, A. (1999) Mol. Biol. Evol. 16, 909–921. [DOI] [PubMed] [Google Scholar]
  39. [42]Scheinker, V. S., Lozovskaya, E. R., Bishop, J. G., Corces, V. G. & Evgen'ev, M. B. (1990) Proc. Natl. Acad. Sci. USA 87, 9615–9619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. [43]Malik, H. S. & Eickbush, T. H. (1999) J. Virol. 73, 5186–5190. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. [44]Malik, H. S., Henikoff, S. & Eickbush, T. H. (2000) Genome Res. 10, 1307–1318. [DOI] [PubMed] [Google Scholar]
  42. [45]Petrov, D. A. (2001) Trends Genet. 17, 23–28. [DOI] [PubMed] [Google Scholar]
  43. [46]Dimitri, P. & Junakovic, N. (1999) Trends Genet. 15, 123–124. [DOI] [PubMed] [Google Scholar]
  44. [47]Tissier, A. F., Marillonnet, S., Klimyuk, V., Patel, K., Torres, M. A., Murphy, G. & Jones, J. D. (1999) Plant Cell 11, 1841–1852. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. [48]Parinov, S., Sevugan, M., De, Y., Yang, W. C., Kumaran, M. & Sundaresan, V. (1999) Plant Cell 11, 2263–2270. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. [49]Berezikov, E., Bucheton, A. & Busseau, I. (2000) Genome Biol. 1, 1–15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. [50]Bowen, N. J. & McDonald, J. F. (2001) Genome Res. 11, 1527–1540. [DOI] [PMC free article] [PubMed] [Google Scholar]

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Authors
Kapitonov, V. V., & Jurka, J.
Affiliations
  • Genetic Information Research Institute (US)
  • University of Arizona (US)
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2003-05-12
Volume
100
Issue
11
Pages
6569-6574
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
DOI
10.1073/pnas.0732024100
PMC
PMC164487
OpenAlex
W2070797653
Cited by
288
References
51
Citations by year
2026: 6 · 2025: 8 · 2024: 12 · 2023: 10 · 2022: 9 · 2021: 10 · 2020: 7 · 2019: 8 · 2018: 6 · 2017: 9 · 2016: 7 · 2015: 9 · 2014: 15 · 2013: 12 · 2012: 12
FWCI
23.19
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health
  • U.S. National Library of Medicine (P41LM006252, 2 P41 LM 06252-04A1)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
Keywords
transposable elements, DNA transposons, Drosophila melanogaster, Anopheles gambiae, P element, Helitrons, horizontal transfer, transposon distribution, transposase
MeSH terms
Amino Acid Sequence, Animals, DNA Transposable Elements, Drosophila melanogaster, Molecular Sequence Data, Paleontology, Phylogeny, Genome, Sequence Homology, Amino Acid, Evolution, Molecular

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