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The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective

Joshua S Kaminker18, Casey M Bergman28, Brent Kronmiller27, Joseph Carlson2, Robert Svirskas3, Sandeep Patel2, Erwin Frise2, David A Wheeler5, Suzanna E Lewis1, Gerald M Rubin124, Michael Ashburner6* and Susan E Celniker2

Author Affiliations

1 Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA

2 Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

3 Amersham Biosciences, 2100 East Elliot Rd, Tempe, AZ 85284, USA

4 Howard Hughes Medical Institute

5 Human Genome Sequencing Center and Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA

6 Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK

7 Current address: Department of Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA

8 These authors contributed equally to this work

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Genome Biology 2002, 3:research0084-0084.20  doi:10.1186/gb-2002-3-12-research0084


This article is part of a series of refereed research articles from Berkeley Drosophila Genome Project, FlyBase and colleagues, describing Release 3 of the Drosophila genome, which are freely available at http://genomebiology.com/drosophila/.

Published: 23 December 2002

Abstract

Background

Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project has provided precise sequence for the repetitive elements in the Drosophila euchromatin. We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species.

Results

We identified 85 known and eight novel families of transposable element varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence. More than two-thirds of the transposable elements are partial. The density of transposable elements increases an average of 4.7 times in the centromere-proximal regions of each of the major chromosome arms. We found that transposable elements are preferentially found outside genes; only 436 of 1,572 transposable elements are contained within the 61.4 Mb of sequence that is annotated as being transcribed. A large proportion of transposable elements is found nested within other elements of the same or different classes. Lastly, an analysis of structural variation from different families reveals distinct patterns of deletion for elements belonging to different classes.

Conclusions

This analysis represents an initial characterization of the transposable elements in the Release 3 euchromatic genomic sequence of D. melanogaster for which comparison to the transposable elements of other organisms can begin to be made. These data have been made available on the Berkeley Drosophila Genome Project website for future analyses.