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Diversity and species concept of the Vischeria/Eustigmatos complex (Eustigmatophyceae)
Procházková, Kateřina ; Eliáš, Marek (advisor) ; Oborník, Miroslav (referee)
Vischeria and Eustigmatos are closely related genera occurring in terrestrial habitats. These genera were distinguished by the differences in the features of the cell wall (projections and ridges of different form, smooth surface respectively). Up to date three species of the genus Eustigmatos and twelve species of the genus Vischeria have been described, but nine of the Vischeria species have been rarely, if ever, observed since the original description. This work is focused on evaluating molecular variability, diversity, and taxonomy of the Vischeria/Eustigmatos complex. Ninety seven strains, obtained from public algal collections or newly isolated from localities from all over the world, were studied, including the type strains of two Eustigmatos species and three Vischeria species. Phylogenetic analyses of the ITS2 rDNA and rbcL sequences showed that these genera are not genetically separated. The five types strains each represented a separate evolutionary lineage. Some of the additional lineages included strains morphologically corresponding to the species Eustigmatos magnus. Some of the newly isolated strains are according to the markers examined genetically indistinguishable from known strains from public algal collections. However, some of them are new lineages. Only one of the phylogenetic...
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Morphological, ultrastructural, and transcriptomic characterization of the newly discovered protist lineage SUM-K
Valt, Marek ; Čepička, Ivan (advisor) ; Oborník, Miroslav (referee)
Here I am presenting a novel deep-branching organism, flagellate SUM-K. SUM-K is morphologically inconspicuous protists that occurs in two distinctive forms, immotile "sun- like" form and motile, flagellated form. Sun-like cells are rounded approximately 5 µm big cells that produce numerous thin radial projections artificially resembling Heliozoeans. Based on ultrastructure analysis and light microscopy observations we classified these projections as novel type of extrusomes with putative function of prey predation. Flagellate state moves with one anterior, posterolaterally directed flagellum. The posterior end of the cell bears a long extrusion that resembles a flagellum but is not motile. Based on these morphological characteristics organism can't be classified into any of the establish eukaryotic supergroups. Likewise, phylogenetic analysis based on SSU rDNA failed to resolve its evolutionary position, placing it to relation with Ancoracysta twista, an orphan lineage similarly unclassifiable to any of current eukaryotic supergroups. Robust analysis based on 206 orthologous genes placed SUM-K to relation with Hemimastigophora. Even though the morphology of currently described Hemimastigophoreans and organism SUM-K is incongruent, its relation presents interesting prospective of evolution of...
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Diversity and evolution of anaerobic Heterolobosea
Pánek, Tomáš ; Čepička, Ivan (advisor) ; Oborník, Miroslav (referee) ; Vávra, Jiří (referee)
9 ABSTRACT This thesis is focused on the phylogeny, diversity, and cell structure of obligately anaerobic Heterolobosea (Excavata: Discoba). Using culture-based approach, we have discovered their hidden species diversity and described 11 new species. Our phylogenetic analyses showed that obligately anaerobic heteroloboseans evolved at least twice independently (Creneidae and Psalteriomonadidae). Psalteriomonadidae is a major anaerobic lineage of Heterolobosea as it includes 16 species and 5 genera. Most psalteriomonadids have acristate mitochondria, although Pseudoharpagon pertyi probably possesses remnants of mitochondrial cristae. Creneidae are represented just by a single species, Creneis carolina, which displays unique cell structure and life cycle. Architecture of its flagellar apparatus is not readily comparable with any other eukaryotes and at least some cytoskeletal elements have undergone unprecedented evolutionary positional changes. Anaerobic heteroloboseans are just rarely detected by environmental, culture-independent approaches. Thus, it is impossible to estimate their real species diversity. Nevertheless, our current data on anaerobic jakobids, another lineage of Discoba, indicates that the culture-based approach is relatively powerful to discover species diversity of anaerobic excavates. In...
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Diversity and evolution of anaerobic Heterolobosea
Pánek, Tomáš ; Čepička, Ivan (advisor) ; Oborník, Miroslav (referee) ; Vávra, Jiří (referee)
9 ABSTRACT This thesis is focused on the phylogeny, diversity, and cell structure of obligately anaerobic Heterolobosea (Excavata: Discoba). Using culture-based approach, we have discovered their hidden species diversity and described 11 new species. Our phylogenetic analyses showed that obligately anaerobic heteroloboseans evolved at least twice independently (Creneidae and Psalteriomonadidae). Psalteriomonadidae is a major anaerobic lineage of Heterolobosea as it includes 16 species and 5 genera. Most psalteriomonadids have acristate mitochondria, although Pseudoharpagon pertyi probably possesses remnants of mitochondrial cristae. Creneidae are represented just by a single species, Creneis carolina, which displays unique cell structure and life cycle. Architecture of its flagellar apparatus is not readily comparable with any other eukaryotes and at least some cytoskeletal elements have undergone unprecedented evolutionary positional changes. Anaerobic heteroloboseans are just rarely detected by environmental, culture-independent approaches. Thus, it is impossible to estimate their real species diversity. Nevertheless, our current data on anaerobic jakobids, another lineage of Discoba, indicates that the culture-based approach is relatively powerful to discover species diversity of anaerobic excavates. In...
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Search for the remnant of plastid in the cell of Rhabdomonas sp.
Soukal, Petr ; Hampl, Vladimír (advisor) ; Oborník, Miroslav (referee)
Phylum Euglenozoa contsists of four groups - Euglenoidea, Kinetoplastea, Symbiontida and Diplonemea. Phototrophic euglenids, which constitute a clade, possess green plastid acquired via secondary endosymbiosis from green alga related to recent genus Pyramimonas. According to generally accepted plastid-late hypothesis, the endo- symbiosis took place after split between phototrophic euglenids and all other euglenozo- ans. Endosymbiotic event is always associated with gene transfer from endosymbiont to nuclei of host. Even if the endosymbiont is completely lost we should be able to observe enrichment of the host genome with the genes derived from endosymbiont. Some recent phylogenetic analyses uncovered genes related to green algae in trypanosomas (Kineto- plastea: Trypanosomatida). Based on this observation, authors postulated a hypothesis that the plastid was present already in common ancestor of kinetoplastids and euglenids and was lost in kinetoplastids and some euglenids including osmotrophic Rhabdomonas costata. During analysis of transcriptome of R. costata we found 63 genes, which could originated from green (24 genes) or other (49 genes) algae. In phylogenetic trees only one was robustly related to green and four were robustly related to other algae. Since the number of genes related to...
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Diversity and species concept of the Vischeria/Eustigmatos complex (Eustigmatophyceae)
Procházková, Kateřina ; Eliáš, Marek (advisor) ; Oborník, Miroslav (referee)
Vischeria and Eustigmatos are closely related genera occurring in terrestrial habitats. These genera were distinguished by the differences in the features of the cell wall (projections and ridges of different form, smooth surface respectively). Up to date three species of the genus Eustigmatos and twelve species of the genus Vischeria have been described, but nine of the Vischeria species have been rarely, if ever, observed since the original description. This work is focused on evaluating molecular variability, diversity, and taxonomy of the Vischeria/Eustigmatos complex. Ninety seven strains, obtained from public algal collections or newly isolated from localities from all over the world, were studied, including the type strains of two Eustigmatos species and three Vischeria species. Phylogenetic analyses of the ITS2 rDNA and rbcL sequences showed that these genera are not genetically separated. The five types strains each represented a separate evolutionary lineage. Some of the additional lineages included strains morphologically corresponding to the species Eustigmatos magnus. Some of the newly isolated strains are according to the markers examined genetically indistinguishable from known strains from public algal collections. However, some of them are new lineages. Only one of the phylogenetic...
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Evolution of anaerobic Heterolobosea
Pánek, Tomáš ; Čepička, Ivan (advisor) ; Oborník, Miroslav (referee)
Heterolobosea is a group of mainly free-living amoebae, flagellates and amoeboflagellates closely related to Euglenozoa and Jakobida (supergroup Excavata). At least two heterolobosean lineages have reduced their mitochondria and live in low concentrations of oxygen (Psalteriomonadidae and extremely halophilic Pleurostomum). Moreover, some other presumably anaerobic species have been described in aerobic heteroloboseid genera, but their sequence data are still missing. The aim of this study is to recognize the diversity and phylogenetic position of both already described and novel non-hypersaline anaerobic heteroloboseans. We have isolated and cultivated 34 strains of free-living heterolobosean flagellates, amoebae and amoeboflagellates from freshwater, brackish and marine microoxic/anoxic habitats. 33 of these strains constitute a single clade (Psalteriomonadidae). We recognize 2 new genera and 3 new species. Phylogenetic analysis of SSU rDNA showed the genus Percolomonas is polyphyletic. The similar morphology of species formally placed within the genus Percolomonas is probably plesiomorphic. Finally, the marine strain PC4AM is morphologically unique and its morphology can not be compared with other heteroloboseans and eukaryotes. It is probably the most derived heterolobosean. Its cell structure...
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Molecular Phylogeny of Selected Protists
Kostka, Martin ; Flegr, Jaroslav (advisor) ; Oborník, Miroslav (referee) ; Simpson, Alastair (referee)
Results 1. We sequencedSSU rDNA of Protoopalinaintestinalis, representativeof opalinids,andKarotomorpha,a proteromonaďdwith hithertono moleculardataavailable. Analyses of thesedataconfirmedcloseaffrnityof thetwo families andalsotheparaphylyof proteromonadids- the resultingtopologywas(Proteromonas+(Karotomopha+ Protoopalina)).Slopalinidsbelongedwithin stramenopilesin our analyses. 2. In ouranalyses,thegenusBlastocystis,geneticallyquite variable,formeda sistergroupof slopalinidswithin thegroupof Stramenopila. 3. We sequencesSSU rDNA of two Chilomastixisolates.The sequencesdifferedsubstantiallyin lengthandcomposition,but formeda monophylumin resultingphylogenetictrees. Surprisingly,Retortamona,swÍlsnotreconstructedasa sister groupof Chilomasfrx,butthetwo generaformedaparaphyletic groupfrom which thediplomonadsevolved(withRetortamonas closerto diplomonads).This resultimpliesthattheancestorof diplomonads(includingenteromonads)wasretortamonadidJike. 4. We sequencedandanďyses SSU rDNA of two morphologically well definedamoebae,Mayorella gemmiferaand Saccamoeba limax.We havefoundthatanothersequenceascribedto S.limm andusedin someanalysesprobablyoriginatesfrom a misidontifi€d organism. 5. WohaveprogrammedtheprogramSlowFaster.Itis aunique user-frierrdlytoolleadingauserstep-by-steptbrougbthewhole processof...
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