Sequence signature analysis of chromosome identity in three Drosophila species.
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.


CONCLUSIONS
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.
Stenberg
Per
P
UCMP, Umeå University, Umeå, Sweden. per.stenberg@molbiol.umu.se
Pettersson
Fredrik
F
Saura
Anja O
AO
Berglund
Anders
A
Larsson
Jan
J
D000818:Animals; D002874:Chromosome Mapping; D002875:Chromosomes / Q000648:ultrastructure*; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D004330:Drosophila / Q000235:genetics*; D029721:Drosophila Proteins / Q000737:chemistry; D019143:Evolution, Molecular; D005260:Female; D017344:Genes, Insect; D016678:Genome; D007091:Image Processing, Computer-Assisted; D016018:Least-Squares Analysis; D008297:Male; D015999:Multivariate Analysis; D025341:Principal Component Analysis; D015203:Reproducibility of Results; D012469:Salivary Glands / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013045:Species Specificity
D029721:Drosophila Proteins