The DOI matches its Crossref record; 49 of the 51 references it cites were found in a registry or an index.
Molecular paleontology of transposable elements in the Drosophila melanogaster genome
Open accessAbstract
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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“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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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301
MEGA2: molecular evolutionary genetics analysis software
Kumar, S., Tamura, K., Jakobsen, I. B., & Nei, M. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.12.1244 · Cited by 6,046
The Genome Sequence of Drosophila melanogaster
Adams, M. D., Celniker, S., 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 · doi:10.1126/science.287.5461.2185 · Cited by 5,902
GeneDoc : analysis and visualization of genetic variation
Nicholas, K. B., Nicholas, H. B., & Deerfield, D. W. (1997) · Medical Entomology and Zoology · Cited by 2,456
The Genome Sequence of the Malaria Mosquito Anopheles gambiae
Holt, R. A., Subramanian, G., Halpern, A. L., Sutton, G. G., Charlab, R., Nusskern, D. R., Wincker, P., Clark, A. G., Ribeiro, J. M. C., Wides, R., et al. (2002) · Science · doi:10.1126/science.1076181 · Cited by 2,025
(2007) · Wiley eBooks · doi:10.1128/9781555817954 · Cited by 1,311
Ab initio Gene Finding in Drosophila Genomic DNAPreprint
Salamov, A. A., & Solovyev, V. V. (2000) · Genome Research · doi:10.1101/gr.10.4.516 · Cited by 1,129
Research works printed but not linked: 6
- 10.1016/S0022-2836(05)80360-2 · DOI · Paper page
- Nicholas, K. B., Nicholas, H. B. & Deerfield, D. W. (1997) EMBNET News 4, 1–4.
- Kurenova, E. V., Leibovich, B. A., Bass, I. A., Bebikhov, D. V., Pavlova, M. N. & Danilevskaia, O. N. (1990) Genetika 26, 1701–1712.2178142
- Smit, A. F. A. (2002) Repbase Rep. 2 (1), 35.
- Kapitonov, V. V. & Jurka, J. (2002) Repbase Rep. 2 (6), 21.
- Berezikov, E., Bucheton, A. & Busseau, I. (2000) Genome Biol. 1, 1–15.11178226
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A unified classification system for eukaryotic transposable elements
Wicker, T., Sabot, F., Hua‐Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A. J., Leroy, P., Morgante, M., Panaud, O., et al. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2165 · Cited by 3,159
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
Xu, Z., & Wang, H. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm286 · Cited by 2,625
Evolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium (2007) · Nature · doi:10.1038/nature06341 · Cited by 2,010
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
Ellinghaus, D., Kurtz, S., & Willhoeft, U. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-18 · Cited by 1,623
DNA transposons and the evolution of eukaryotic genomes.
Feschotte, C., & Pritham, E. J. (2007) · Annual Review of Genetics · doi:10.1146/annurev.genet.40.110405.090448 · Cited by 1,218
Metadata
- 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
- 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
- green
- www.ncbi.nlm.nih.gov
- 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 › Biochemistry, Genetics and Molecular Biology › Genetics › 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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