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Background  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  Drosophila . 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  Drosophila  genomes for chromosome-specific sequences.    Results  By combining genome annotations and cytological data with multivariate statistics related to three  Drosophila  genomes we found sequence signatures that distinguish Muller's F-elements (chromosome 4 in  D. melanogaster ) from all other chromosomes in  Drosophila  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  D. melanogaster  motif may be involved in POF-binding to the F-element. In addition, the X-chromosomes of  D. melanogaster  and  D. yakuba  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.    Conclusion  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  Drosophila .

Sequence signature analysis of chromosome identity in three Drosophila species.