Promoter variation in the ribosomal RNA genes inDrosophila melanogasterstrains

The sequences of thirty D. melanogaster ribosomal DNA promoter regions have been determined. Fifteen of these were isolated from a wild population recently captured in North Wootten, England. The other fifteen were isolated from an inbred laboratory strain. The overall level of variation is almost twice as high in the North Wootten strain as in the inbred laboratory strain. Two mutations at nucleotides -17 and -21 relative to transcription start, fall directly within a region known to be transcriptionally important. The sequences are also compared to eight previously published sequences from another D. melanogaster strain, Oregon R. Two of these eight clones have a -17 mutation identical to the one found in this study, suggesting that this polymorphism is widespread. Strikingly, all eight of these clones carry two single base pair changes not found in any of the other thirty clones, indicating the extent with which promoter variants can be homogenized and fixed in a population. Polymorphisms show different levels of homogenization within the rDNA unit spacer repeats or between different arrays depending on the location of the polymorphism. This has implications for the evolution of the observed species-specific transcription of ribosomal RNA genes.