Background: The intergenic spacer of the ribosomal genes in eukaryotes (IGS) contains duplications of the core transcription promoter. The number of these duplicated promoters, as measured by the IGS length, appears to be correlated with growth rate and development time in several distantly related taxa. In the present study, we examined IGS length variation across a number of species of Drosophila to determine the amount of variation in this trait across different evolutionary time scales. Furthermore, we compared the usefulness of two methods commonly used to determine IGS length: Southern Blot Hybridization (SB) and Polymerase Chain Reaction (PCR).
Results: Our results show broad variation in IGS length across the genus Drosophila, but closely related species had similar IGS lengths. Our results also suggest that PCR tends to underestimate the true IGS size when the size is greater than 5 kb, and that this degree of underestimation is greater as the IGS size increases.
Conclusion: Broad variation in IGS length occurs across large evolutionary divergences in the subfamily Drosophilinae. Although average IGS length has been shown to evolve rapidly under artificial selection, closely related taxa generally have similar average IGS lengths. Our comparison of methods suggests that without previous knowledge of the DNA sequence of the IGS and flanking regions, both methods be used to accurately measure IGS length.