An Evaluation of the Use of the LSU rRNA D1-D5 Domain for DNA-based Taxonomy of Eukaryotic Protists

Diagnostic signature DNA sequences are important tools for the identification of species. There is an active debate in the literature on the choice of the best markers applicable for a broad range of organisms. Protists have seldom been included in these evaluations. Mitochondrial gene sequences are inappropriate for protists since several groups do not possess mitochondria. Here we studied the application of the large subunit (LSU) rRNA gene fragments (D1-D5) regarding their usefulness to discriminate between a wide range of heterotrophic nanoflagellates. Phylogenetic analyses based on the LSU rRNA fragments showed similar results compared to phylogenetic trees based on the small subunit (SSU) rRNA. The data set indicates the power of the use of the D1-D5 region as a marker for a DNA-based taxonomy. Our results, together with the available sequences in Genbank, form a comprehensive database for unicellular eukaryotes, especially heterotrophic flagellates. It is now possible to assign new sequences to the different groups of heterotrophic flagellates which we have tested for different closely related Cercomonas and Paracercomonas strains from groundwater.