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

By J. Kaminker, Casey M. Bergman, B. Kronmiller, Joseph W. Carlson, Rob Svirskas, Sandeep Patel, Erwin Frise, D. Wheeler, Suzanna Lewis, Gerald M. Rubin and 2 more. Genome Biology, 2002

602 citations recorded by the source corpus.

BackgroundTransposable 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.ResultsWe 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.ConclusionsThis 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.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/02f1247df6758224cde5a345ce475bafc36b4342

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Citations in the corpus

Dopamine Is a Regulator of Arousal in the Fruit Fly (2005, background): “Sequencing of the fmn dDAT cDNA revealed that there was no splicing at the exon 6 –intron 6 junction, as a result of an insertion of the 5 portion of a roo transposon (Kaminker et al., 2002) into intron 6.”
Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. (2003, background): “…temporal contexts of origin and horizontal transfer events of the transposable elements, and understanding timing of gene duplications, chromosomal changes, and evolution of genome anatomies in general (Petrov and Hartl 1998; Silva and Kidwell 2000; Bergman et al. 2002; Kaminker et al. 2002).”
FlyBase: genes and gene models (2004, methodology): “0 at the time of writing (5–7), has been enhanced by hand curation of all gene models (8,9), including integration of error reports submitted by the user community.”
Fast Computation and Applications of Genome Mappability (2012, background): “Indeed, among repeat elements of class I the fly genome does not contain non-LTR retrotransposons such as SINEs [17], whereas the proportion of LTR retrotransposons constitutes more than one third of the total proportion of repeats ( 10 : 46% versus 26 : 50% ; see Table 2).”
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review (2002, methodology): “Details of these analyses are reported in an accompanying article [18].”
The origin of new genes: glimpses from the young and old (2003, background): “Several factors, such as a hypothetical difference in transcription rates, recombination rates, mutation rates and negative selection against insertion, have all been tested and found to be irrelevant as they do not differ significantly between the X chromosome and the autosome”
Combined Evidence Annotation of Transposable Elements in Genome Sequences (2005, methodology): “To allow direct comparison with previous results [18], we used the Release 3 genomic sequence as a query to be scanned for similarity to reference sequences in version 7.”
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons (2008, methodology): “The high quality annotations of transposable elements in Saccharomyces cerevisiae [25] and of Drosophila melanogaster [26] illustrate such species specific constraints.”
The small RNA profile during Drosophila melanogaster development. (2003, background): “…1C). elements corresponding to 40% of all known transposIn mouse and human, the gene cluster underwent dupli- able elements in D. melanogaster (Kaminker et al., 2002). cation and the distance between miRNA genes was in- The most frequently cloned rasiRNAs were derived from creased further…”