On The Moleculer Phylogeny Of Seven Subclasses In The Phylum Cfliophora

In the past20years, the study for origin and evolution of eukaryotes were welldeveloped based on phylogenies of small subunit ribosomal RNA genes. More recently,the eukaryote tree of life were strongly influenced by synthesis of analyses of sequencedata for rRNAs, concatenated sets of conserved proteins and organellar genomes, andsome detailed ultrastructural comparisons. This tree is thought to be more close to the reallife tree. Among these, ciliate is one clade of the “Alveolata” group of eukaryotes.Molecular phylogeny suggests it is a well supported monophyly. Ciliates have two kindsof nuclears, complicated organelles and cytoskeleton structures (i. g. cilia, membranes),and unique sexual reproduction (conjugation), they are thought to be the mostcomplicated organisms among the protists groups. Thus they become important forresearchers who are interested in cell biology, genetics and studies on relationshipsbetween nucleus and cytoplasm, parasitic/commensal ecologics, and especially in theeukaryotic biological evolution. However, although they play such important roles in theeukaryotic studies, the fundamental studies, like systematics and phylogenetics on theciliated protozoa are not as developed as other well known eukaryotic groups, i. g.Amoebozoa, Rhizaria, Excavata. Wider taxa sampling and further more molecularinformation available to be a background for ciliates’ phylogeny is urgent. As far as weknow, the substantial studies in ciliated protozoa only focused on Paramecium,Tetrahymena, and Oxytricha which are easily cultured and have bigger cell size. Howeverrare comprehended studies have been performed for the kinetofragminophore ciliatessensu Coliss (include i.g. Litostomatea, Prostomatea, Nassophorea, Colpodea), which arenamely primary but occupy a high diversity of the ciliate world. These organisms aresmaller or difficult to identify using modern taxonomic techniques and hardly to becultured, which to a large degree limit the substantial studies, although their higherdiversity and important roles in the ciliates evolution. This makes it inevitable tocomplement information for them. On the other hand, the systematics still remains confusing as regards to the evolutionary relationship in many well-known groups, i. e.Oligohymenophorea and Spirotrichia, due to the high diversity of their morphology, thecomplicated life style and the disequilibrium weight put into morphologic structures bydifferent taxonomists, and the insufficient molecular information.In the recent10years, the development of gene sequencing technique, improvementof methods for ciliates molecular study and ameliorate of bioinformatics analyses, havemade it reliable to modify and complement the systematics and phylogeny among thewell known and unknown ciliates groups. In this work, we studied7ciliates groups onsubclass level, using single gene phylogeny, multigene, gene analyses, secondarystructural analyses, predicted topology test and ARDRA methods. Our work resolvedsome confusions of morphological taxonomy and phylogenetic positions of some keytaxa at the genetical level. New proposals are also suggested based on the updated datasetand some of these challenged the traditional views.These conclusions were confirmed:1Phylogeny of class LitostomateaMultigene phylogeny for13genera19species of subclass Haptoria, including totally51new sequences)(1) Cyclotrichium and Paraspathidium were clearly separated from the haptoridsand even from class Litostomatea, rejecting their high-level taxonomic assignmentsbased on morphology.(2) The secondary structures of the variable regions2and4of Paraspathidium,and V4region of Cyclotrichium are similar to those of the plagiopyleans andprostomateans but differ from the hapotrids in Helix10, Helix E10-1and Helix E23-5.Paraspathidium also has a distinct pattern in Helix E23-7.(3) Cyclotrichium and Paraspathidium branch instead with the classesPlagiopylea, Prostomatea and Oligohymenophora. This raises the possibility that thewell-known but phylogenetically problematic cyclotrichiids Mesodinium andMyrionecta may also have affinities here, rather than with litostomes.(4) The transfer of Trachelotractus to Litostomatea is supported, especially by theanalyses of SSU rRNA and LSU rRNA genes; however Trachelotractus and Chaenea(more uncertainly) generally form the two deepest lineages within litostomes.(5) Phylogenies of the new molecular markers are consistent with SSU rRNAgene information in recovering order Pleurostomatida as monophyletic; it has a higherdiversity on the family level than the tridational morphological schemes, but subclassTrichostomatia still emerges in the Haptorida clade. 2Phylogeny of class Oligohymenophorea(1) Paratetrahymena and Cardiostomatella vermiformis formed a moderatelywell-supported clade that diverged at a deep level from all other scuticociliates,supporting separation of loxocephalids from other scuticociliates as a suprafamilialtaxon.(2) Cinetochilum is closest to the subclass Apostomatia, the genus Sathrophilus,together with Anoplophrya, a poorly known Astomatia, forms two peripheral branchesseparated from the scuticociliatian assemblage(3) The morphological and morphogenetic similarities of loxocephalids tohymenostomes may be plesiomorphies, and the conflicting mix of scuticociliate andhymenostome characteristics seen in loxocephalids may result from differing rates ofcharacter evolution.(4) Dexiotrichides pangi and Urocentrum formed a small clade that associatedwith hymenostomes and peritrichs, although their phylogenetic positions areinfluenced by a combination of heterogeneous data and long-branch attraction causedby poor representation of taxa in analyses.(5) The well known genus Cyclidium, a member of the order Pleuronematida, wasrevealed to be polyphyletic as a byproduct of our analyses of loxocephalids.3Phylogeny of class Spirotrichea(1) SSU rRNA gene sequence analyses match the recent findings about themolecular evolution of oligotrichs, indicating that the family Strombidiidae isparaphyletic, so does the genus Strombidium.(2) Genus Omegastrombidium is separated from the Genus Strombidium, asshown in recent sadistic analyses; morphospecies in Genus Novistrombidium, based onsimilarity of somatic ciliature, are separated from each other in all topological trees,indicating that this genus cold be a paraphyletic group.(3) The similarities of the SSU rRNA gene of specimens identified asStrombidium sulcatum and S. inclinatum are99.8%–100%.(4) Phylogenetic analysis inferred from the ARDRA reprinting patterns indicatesthat Diophrys and Diophryopsis showed relatively close relationship, whileParadiophrys usually clustered at the basal of the root. The result indicates thatDiophrys and Diophryopsis formed a sister clade, while Paradiophrys is more closelyrelated to Uronychia, suggesting that the Diophrys complex species evolved as aparaphyletic group.4On an amitochondriate Trimastix marina(1) A marine isolate of Trimastix marina was studied for the first time combining light microscopic, electron-microscopic and molecular phylogenetic methods.(2) These results indicate a paraphyly of Trimastix as currently understood, andlikely require a revision of genus Trimastix.(3) Marine Trimastix marina is the only known representative of the most basallineage of the Trimastix-oxymonads groups (Preaxostyla/=Class Anaeromonada), and isthus a key organism for comparative biology and evolution of reduced mitochondria inanaerobic excavates.