Isolation and characterization of ribosomal DNA variants from Sciara coprophila

The ribosomal RNA multigene family in the fungus fly Sciara coprophila contains a total of only 65 to 70 repeat units. We explored the types and frequencies of variant repeats in this small multigene family by characterizing different cloned rDNA variants from Sciara. Although we did not observe any intergenic spacer length variants in Sciara, we found a variant due to the insertion of a putative mobile element (lambda Bc11), and variants containing ribosomal insertion elements. By DNA sequence analysis of rDNA/non-rDNA junctions, there are three distinct types of ribosomal insertion elements found in Sciara rDNA: two correspond to the R1 and R2 insertion elements found in other dipterans (clones lambda Bc5 and pBc1L1, respectively), and one is a novel class of ribosomal insertion elements (R3, exemplified by clone pBc6D6) which so far is unique to Sciara. Together, the several different rDNA variants make up from 12 to 20% of the rDNA in Sciara. These results are discussed in the context of evolution of the ribosomal RNA multigene family.