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Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains


Background: Chromosome four of Drosophila melanogaster, known as the dot chromosome, is largely heterochromatic, as shown by immunofluorescent staining with antibodies to heterochromatin protein 1 (HP1) and histone H3K9me. In contrast, the absence of HP1 and H3K9me from the dot chromosome in D. virilis suggests that this region is euchromatic. D. virilis diverged from D. melanogaster 40 to 60 million years ago.

Results: Here we describe finished sequencing and analysis of 11 fosmids hybridizing to the dot chromosome of D. virilis (372,650 base-pairs) and seven fosmids from major euchromatic chromosome arms (273,110 base-pairs). Most genes from the dot chromosome of D. melanogaster remain on the dot chromosome in D. virilis, but many inversions have occurred. The dot chromosomes of both species are similar to the major chromosome arms in gene density and coding density, but the dot chromosome genes of both species have larger introns. The D. virilis dot chromosome fosmids have a high repeat density (22.8%), similar to homologous regions of D. melanogaster (26.5%). There are, however, major differences in the representation of repetitive elements. Remnants of DNA transposons make up only 6.3% of the D. virilis dot chromosome fosmids, but 18.4% of the homologous regions from D. melanogaster; DINE-1 and 1360 elements are particularly enriched in D. melanogaster. Euchromatic domains on the major chromosomes in both species have very few DNA transposons (less than 0.4 %).

Conclusion: Combining these results with recent findings about RNAi, we suggest that specific repetitive elements, as well as density, play a role in determining higher-order chromatin packaging.

Repeat analysis of D. virilis contigs compared to the D. melanogaster genome. The repeat density, defined as the percentage of total sequence (in base-pairs) that has been annotated as repetitive has been calculated using the D. virilis fosmid sequence obtained in this study and homologous regions from D. melanogaster (see Materials and methods). D. melanogaster and D. virilis have a very similar low repeat density on the major chromosome arms, and a similar but much higher repeat density on the dot chromosomes. (a) Percent repeat for each type identified by RepeatMasker using RebBase 8.12 with additional repeats identified in a BLASTN all-by-all comparison of the fosmid sequences presented here. (b) Percent repeat for each type identified by RepeatMasker using the Superlibrary (see text for description). The dot chromosome of D. melanogaster has about three times more DNA transposon sequence than does the D. virilis dot chromosome. 'Unknown' repeats are those from both RebBase 8.12 and the D. virilis PILER-DF library that have not been classified as to type.