Distribution of dinucleotide microsatellites in the Drosophila melanogaster genome

Microsatellites, a special class of repetitive DNA, have become one of the most popular genetic markers. The progress of various genome projects has m ade it possible to study the genomic distribution of microsatellites and to evaluate the potential influence of several parameters on their genesis. W e report the distribution of dinucleotide microsatellites in the genome of Drosophila melanogaster. When considering only microsatellites with five or mure repeat units, the average length of dinucleotide repeats in D. melano gaster is 6.7 repeats. We tested a wide range of parameters which could pot entially influence microsatellite density, and we did not detect a signific ant influence of recombination rate, number of exons, or total length of co ding sequence. In concordance with the neutral expectation for the origin o f microsatellites. a significant positive correlation between AT content an d (AT/TA)(n) microsatellite density was detected. While this pattern may in dicate that microsatellite genesis is a random process, we also found evide nce for a nonrandom distribution of microsatellites. Average microsatellite density was higher on the X chromosome, but extreme heterogeneity was obse rved between different genomic regions. Such a clumping of microsatellites was also evident on a more local scale, as 38.9% of the contiguous sequence s analyzed showed a deviation from a random distribution of microsatellites .