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Evolution of the genetic code and classification of oxymonads
Šrámová, Eliška ; Hampl, Vladimír (advisor) ; Čepička, Ivan (referee)
Oxymonads are a group of heterotrophic flagellates living in low oxygen environment. These protists inhabit mainly the gut of xylophagous insects (cockroaches, termites), with an exception of the genus Monocercomonoides, which was described from the intestinal contents of many vertebrates. On the basis of molecular data, Oxymonadida are classified into the supergroup Excavata (Cavalier-Smith, 2002; Simpson et al., 2006, Hampl et al. 2009). This thesis was focused on the diversity of genus Monocecomonoides from the morphologically simplest family Polymastigidae. The main goal of our work was to gather sequence data from strains isolated from a wide spectrum of hosts. We have obtained 26 partial sequences of the gene for the SSU rDNA in total, of which two belonged to another oxymonad, apparently genus Oxymonas. Our phylogenetic analysis indicated that the representatives of the genus Monocercomonoides form one group, however with a low bootstrap support. On the basis of published data about the presence of non-canonical genetic code in some oxymonads (Keeling and Leander, 2003; de Koning et al., 2008), we decided to explore this rare phenomenon in representatives of the genus Monocercomonoides. For this part of the study we gathered 9 partial sequences of α-tubulin gene. In these sequences we have not...
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Phylogeny of Archamoebae
Ptáčková, Eliška ; Čepička, Ivan (advisor) ; Vávra, Jiří (referee)
Archamoebae is a small group of anaerobic protists belonging to the eukaryotic supergroup Amoebozoa. Historically, they were regarded as primitively amitochondriate. However, a mitochondrial remnant has been found in some archamoebae. Phylogenetic analyses showed that Archamoebae are closely related to the aerobic slime moulds (Mycetozoa). Trophozoites of archamoebae are amoeboflagellates or aflagellated amoebae. The group includes both parasitic (Entamoeba, Endolimax and, possibly, Endamoeba and Iodamoeba) and free-living (Mastigamoeba, Mastigella, Pelomyxa) genera. The genus Mastigina comprises both endozoic and free-living representatives. Flagellated genera Mastigina, Mastigamoeba, Mastigella and Pelomyxa possess a single basal body associated with a microtubular cone which may or may not be associated with nucleus. The cone is a common feature for Archamoebae and mycetozoan slime moulds. The phylogeny of Archamoebae has not been fully elucidated yet and the taxonomy of free-living representatives is confusing. In the present study, we obtained 42 stable isolates of free-living Archamoebae. We sequenced and analyzed SSU rDNA of 15 of them. The Archamoebae split into five lineages. Based on TEM, we were able to recognize genera Mastigamoeba and Mastigella. The isolate IND8 probably represents a new...
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Evolution of the genetic code and classification of oxymonads
Šrámová, Eliška ; Hampl, Vladimír (advisor) ; Čepička, Ivan (referee)
Oxymonads are a group of heterotrophic flagellates living in low oxygen environment. These protists inhabit mainly the gut of xylophagous insects (cockroaches, termites), with an exception of the genus Monocercomonoides, which was described from the intestinal contents of many vertebrates. On the basis of molecular data, Oxymonadida are classified into the supergroup Excavata (Cavalier-Smith, 2002; Simpson et al., 2006, Hampl et al. 2009). This thesis was focused on the diversity of genus Monocecomonoides from the morphologically simplest family Polymastigidae. The main goal of our work was to gather sequence data from strains isolated from a wide spectrum of hosts. We have obtained 26 partial sequences of the gene for the SSU rDNA in total, of which two belonged to another oxymonad, apparently genus Oxymonas. Our phylogenetic analysis indicated that the representatives of the genus Monocercomonoides form one group, however with a low bootstrap support. On the basis of published data about the presence of non-canonical genetic code in some oxymonads (Keeling and Leander, 2003; de Koning et al., 2008), we decided to explore this rare phenomenon in representatives of the genus Monocercomonoides. For this part of the study we gathered 9 partial sequences of α-tubulin gene. In these sequences we have not...
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Cryptic diversity of free-living trichomonads and their phylogenetic position within Parabasalia
Céza, Vít ; Čepička, Ivan (advisor) ; Hampl, Vladimír (referee)
Trichomonads (Parabasalia) are anaerobic microeukaryotes classified in the supergroup Excavata. Inclusion of parabasalids within Excavata is exclusively based on the molecular- phylogenetic evidence. Over 400 species of parabasalids have been described so far, and the vast majority of them are endobiotic. In contrast, only few species of free-living parabasalids forming four independent lineages have been described (Pseudotrichomonas keilini, Ditrichomonas honigbergii, Monotrichomonas carabina, Honigbergiella sp., Tetratrichomonas undula, and Lacusteria cypriaca). Lacusteria cypriaca is a new species and genus described in our recent paper. In this paper we published the first two sequences of SSU rDNA from Pseudotrichomonas keilini as well. All of these lineages are likely secondarily free-living, and they developed from endobiotic ancestors. In addition to the already published Lacusteria cypriaca and Pseudotrichomonas keilini strains, we have recently obtained seven another isolates of free-living trichomonads (LAGOS2D, E2NT, CK, LAGOS2M, GR8, GOU23 LIVADIAN, and VAV1A1); from all of these isolates we sequenced SSU rDNA and performed phylogenetic analyses. These isolates split into four independent evolutionary lineages, which indicate that free-living parabasalids are more diversed and...
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Phylogeny of Archamoebae
Ptáčková, Eliška ; Vávra, Jiří (referee) ; Čepička, Ivan (advisor)
Archamoebae is a small group of anaerobic protists belonging to the eukaryotic supergroup Amoebozoa. Historically, they were regarded as primitively amitochondriate. However, a mitochondrial remnant has been found in some archamoebae. Phylogenetic analyses showed that Archamoebae are closely related to the aerobic slime moulds (Mycetozoa). Trophozoites of archamoebae are amoeboflagellates or aflagellated amoebae. The group includes both parasitic (Entamoeba, Endolimax and, possibly, Endamoeba and Iodamoeba) and free-living (Mastigamoeba, Mastigella, Pelomyxa) genera. The genus Mastigina comprises both endozoic and free-living representatives. Flagellated genera Mastigina, Mastigamoeba, Mastigella and Pelomyxa possess a single basal body associated with a microtubular cone which may or may not be associated with nucleus. The cone is a common feature for Archamoebae and mycetozoan slime moulds. The phylogeny of Archamoebae has not been fully elucidated yet and the taxonomy of free-living representatives is confusing. In the present study, we obtained 42 stable isolates of free-living Archamoebae. We sequenced and analyzed SSU rDNA of 15 of them. The Archamoebae split into five lineages. Based on TEM, we were able to recognize genera Mastigamoeba and Mastigella. The isolate IND8 probably represents a new...
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Phylogeny of amoebae of family Flabellulidae
LISNEROVÁ, Martina
This thesis deals with one of little groups of amoeboid protozoa family Flabellulidae of Amoebozoa group (Lobosa, Tubulinea). This group has only one cell with one or many nuclei. Body is not covered by shell or scales, but only with glycocalyx. They move by using lobopodias, the movement being based on actin-myosin complex. Family Flabellulidae includes currently the genera Flabellula and Paraflabellula, historically genus Flamella. We lack sufficient information about phylogeny of family Flabellulidae. New sequences of actin genes, SSU rRNA and COX1 from members of family Flabellulidae were obtained in this study and the relationships between family Flabellulidae and other hierarchical groups are also discussed.
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