Phylogenetic Study Of Urostylid And Cyrtophorid Ciliates Using Nuclear SSUrRNA Secondary Structure And Mitochondrial SSUrRNA Gene

Ciliates (Ciliophora. Protista) are one kind of the most complex and differentiated single cell organisms. They play very important roles in cell biology, eukaryotic genetics, evolution and many other fields since their complicated morphogenetic process, unique sexual reproduction and special nuclear dualism. But we have not yet known quite well about this kind of organism for a long time due to many reasons such as short of experiment technique limit. As the modern silver-staining techniques and molecular techniques developed, some taxa got studied and clearly defined while most ciliates are still in confusion. Progresses of ciliate ecological or behavior studies are very slowly mainly because of the lack of identification materials, molecular information and undersampling. So based on previous studies on ciliate phylogenetics and morphological studies, we further develop some more molecular markers for studying some taxa’s evolutionary positions.(1) A case study to estimate the applicability of secondary structures of SSU rRNA gene in taxonomy and phylogenetic analyses of ciliatesPhylogenetic studies of ciliates are mainly based on the primary structure information of the nuclear genes. Some regions of the small subunit ribosomal RNA (nSSU rRNA) gene have distinctive secondary structures, which have demonstrated value as phylogenetic/taxonomic characters. In the current work, we predict the secondary structures of four variable regions (V2, V4, V7 and V9) in the SSU-rRNA gene of 45 urostylids. Structure comparisons indicate that the V4 region is most effective in revealing interspecific relationships, while the V9 region appears suitable at the family level or higher. The V2 region also offers some taxonomic information, but is too conserved to reflect phylogenetic relationships. Finally, the V7 region is the least informative. We constructed several phylogenetic trees, based on the primary sequence alignment and based on an improved alignment according to the secondary structures. The results suggest that including secondary structure information in phylogenetic analyses provides additional insights into phylogenetic relationships. Using urostylid ciliates as an example, we show that secondary structure information results in a better understanding of their relationships.(2) Phylogenetic study of ciliates using mtSSUrRNA gene with a focus on cyrtophorid ciliatesApart from the nSSUrRNA gene based study, mtSSUrRNA gene also has potential to be used as molecular markers for ciliate phylogenetic study. Phylogenetic studies based on a single locus may not be able to reflect the true relationships while multiloci studies can be more persuasive. In this study, mtSSUrRNA gene is used for phylogenetic analyses. With a focus on Cyrtophorida and Nassophorea, we did a broad sample and the result shows that (1) mtSSUrRNA gene is a good molecular marker for ciliate phylogenetics which could show more close relationships than nSSUrRNA gene; (2) although with low support values in the mtSSU rRNA gene tree, a two-gene concatenated tree could solve this problem with higher support values; (3) the genus Brooklynella is intermediate between Dysteriidae and Hartmannulidae; (4) the genus Trithigmostoma is supposed to remain in the family Chilodonellidae (5) the genus Zosterodasy is not monophyletic according to mtSSUrRNA gene analyses which corresponds to the nSSUrRNA gene analyses; (6) the high variety of mtSSUrRNA gene could be able to explore cryptic species and help to know more about ciliate biodiversity.