Analysis of the internal transcribed spacer 2 (ITS2) region of scuticociliates and related taxa (Ciliophora, Oligohymenophorea) to infer their evolution and phylogeny.

The ITS2 (ITS--internal transcribed spacer) region of the rDNA in 11 representative scuticociliates and two ambiguously related genera was analyzed. In common with other eukaryotes, the putative ITS2 folding pattern consists of a closed loop with four helices supported by minimum free energy and compensatory base changes (CBCs), although two of these helices are variable and sometimes absent. Three topologies were obtained on the basis of traditional primary sequence analysis, "string" strategy of secondary structure and analysis of the combined data. It was found that the secondary structure information could help to improve alignment and utilize appropriately phylogenetic strategies. The proposed phylogenies, though differing between sequence- and structure-based results, provide consistent support for high-level clades: the systematically questionable genera Dexiotrichides and Cardiostomatella always cluster together in a clade basal to the scuticociliates s.s., whereas Pleuronema branches from other uronematids at a deep level, and is hence a divergent taxon. Within the well-supported monophyletic philasterids, a sister relationship exists between Orchitophrya and Mesanophrys, while Uronema shows a close relationship with the group including Paranophrys and Parauronema. The positions of Metanophrys, Pseudocohnilembus and Anophryoides among the philasterids remain poorly resolved. Our findings firmly support the proposed evolutionary scenario inferred previously both from morphological and molecular data.