Abstract
An analysis of high-resolution transposable element annotations in Drosophila melanogaster suggests the existence of a global surveillance system against the majority of transposable elements families in the fly.
Highlights
Most eukaryotic genomes contain a substantial fraction of middle repetitive, transposable element (TE) sequences interspersed with the unique sequences encoding genes and cis-regulatory elements
Of genome). (We note that the proportion of the Release 4 genome estimated here as TE is calculated as the sum of nonredundant annotation spans including unique sequences inserted into TEs; this procedure differs slightly from our previous estimates for Release 4, which only included sequences strictly homologous to TE query sequences [10].) The discrepant changes in these two metrics of TE abundance across releases results from the fact that almost all new TEs in Release 4 are either small fragments and/or annotations of the highly abundant but degenerated INE-1 element [14], a family that was omitted from the Release 3 annotation
By accounting for the non-random distribution of TEs across the genome, we provide an accurate estimate of TE abundance for the vast majority of the genome sequence in highrecombination, non-pericentromeric regions
Summary
Most eukaryotic genomes contain a substantial fraction of middle repetitive, transposable element (TE) sequences interspersed with the unique sequences encoding genes and cis-regulatory elements. The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. As with all unfinished whole-genome shotgun assemblies, uncertainty in the assembly of repetitive DNA in the first two releases of the Drosophila melanogaster genome sequence posed difficulties for analysis of TE sequences [5,6,7,8]. The improved assembly of repetitive regions in the D. melanogaster Release 3 genome sequence presented the first opportunity to study TEs in a finished whole genome shotgun sequence [2,9], revealing the true challenge that these sequences pose for their systematic annotation [10,11]. With further improvements in the Release 4 genome sequence made possible by the efforts of the Berkeley Drosophila
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