Molecular Phylogeny On Scuticociliatia (Ciliophora, Oligohymenophorea)

Scuticociliatia is one of the subclass within the class Oligohymenophorea of the phylum Ciliophora. Scuticociliates distribute in all kinds of water biotopes, especially in the eutrophic aquaculture environments. Taxonomy and systematics among this group remain greatly confuse due to their very small size and similar morphology. Random amplified polymorphic DNA (RAPD), restrict fragment length polymorphism (RFLP) and sequences analysis were used in the present work to discriminate the closely - related taxa and deduce the phylogenetic relationships among taxa within the subclass Scuticociliatia. Different molecular markers and analysis methods used in the work were evaluated.RAPD, RAPDvsRFLP were used to detect the distances among populations, closely - related species and genera, as well as the taxa higher than genus. It shows that RAPD can be well used hi the discrimination at the species and under-species levels, while RFLP patterns are species-specific so that it can distinguish species and reveal their genetic relationships at species level.The small subunit rRNA (SSrRNA) gene sequences for 10 strains of 9 species within the subclass Scuticocilitia were determined, and submitted to the GenBANK/EMBL database. These sequences are in the majority in all the sequences from this subclass collected in the GenBANK/EMBL database. The ITS1-5.8S-ITS2 gene sequences for 9 strains of 8 scuticociliates were determined. The phylogeny of Scuticociliatia were deduced based on these four sequences, SSrRNA, ITS1, ITS2 and 5.8S with the neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) methods. The conclusions were confirmed at the molecular level that:1 . The subclass Scuticociliatia is a monophyly, which is phylogenetically closed to the subclass Hymenostomatia within the class Oligohymenophorea.2. The order Philasterida sensu Lynn and Small (1997) is also a monophyly separated from the species within the order Pleuronematida.3. The genera Uronema and Parauronema are polyphyly, the species in which show different phylogenetic relationships from that in morphological taxonomy.4. The morphologically closely - related genera, Paranophrys, Mesanophrys and Metanophrys also show close relationships in the molecular phylogenetic tree.5. The molecular analysis didn't support the separation between the families, Philasteridae and Cohnilembidae in Corliss (1979) system.6. Dexiotrichides pangi is placed in the edge of the Scuticociliatia. It's regarded as an in-between species of Scuticociliatia and Hymenostomatia.Comparison among phylogenetic trees on different sequences show that 5.8S rRNA gene canrf t be used to construct the phylogenetic tree for relatively lower taxa, while ITS1 and ITS2 are fit for discrimination between the lower taxa and their systematic reconstruction. SSrRNA gene is the most appropriated among the four for the systematic studies considering their length and conservation.