<p>Abstract</p> <p>Background</p> <p>All eukaryotic organisms need to distinguish each of their chromosomes. A few protein complexes have been described that recognise entire, specific chromosomes, for instance dosage compensation complexes and the recently discovered autosome-specific Painting of Fourth (POF) protein in <it>Drosophila</it>. However, no sequences have been found that are chromosome-specific and distributed over the entire length of the respective chromosome. Here, we present a new, unbiased, exhaustive computational method that was used to probe three <it>Drosophila </it>genomes for chromosome-specific sequences.</p> <p>Results</p> <p>By combining genome annotations and cytological data with multivariate statistics related to three <it>Drosophila </it>genomes we found sequence signatures that distinguish Muller's F-elements (chromosome 4 in <it>D. melanogaster</it>) from all other chromosomes in <it>Drosophila </it>that are not attributable to differences in nucleotide composition, simple sequence repeats or repeated elements. Based on these signatures we identified complex motifs that are strongly overrepresented in the F-elements and found indications that the <it>D. melanogaster </it>motif may be involved in POF-binding to the F-element. In addition, the X-chromosomes of <it>D. melanogaster </it>and <it>D. yakuba </it>can be distinguished from the other chromosomes, albeit to a lesser extent. Surprisingly, the conservation of the F-element sequence signatures extends not only between species separated by approximately 55 Myr, but also linearly along the sequenced part of the F-elements.</p> <p>Conclusion</p> <p>Our results suggest that chromosome-distinguishing features are not exclusive to the sex chromosomes, but are also present on at least one autosome (the F-element) in <it>Drosophila</it>.</p
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