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Bacterial REP elements: origins, variability and application.
Nunvář, Jaroslav ; Lichá, Irena (advisor) ; Pačes, Jan (referee) ; Melter, Oto (referee)
4 ABSTRACT (English) This thesis is based on three published research papers studying bacterial REP (repetitive extragenic palindrome) elements. REP elements are one of the best-characterized groups of bacterial DNA repeats, distributed mostly in gammaproteobacteria, including enterobacteria. They are present in noncoding parts of host genomes, usually occurring in hundreds of copies. REPs are typically aggregated in higher order repeats. In the Gram-negative model Escherichia coli, interactions of several proteins important for cell's physiology with REPs were described, indicating significant role for these elements for host cells. The first work (Nunvar et al. 2010) presents the discovery of a protein class, related to IS200/IS605 transposases. These proteins, termed RAYTs (REP-associated tyrosine transposases), contain characteristic motifs in their amino acid sequences, which are absent in canonical IS200/IS605 transposases. Another attribute of RAYTs is the arrangement of their encoding genes. These are single copy genes, always flanked at both termini by at least two REPs in inverted orientation. Based on the similarity between the REP-rayt-REP unit and insertion sequences of the IS200/IS605 family, between RAYTs and tyrosine transposases and between REPs and subterminal sequences of the IS200/IS605...
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Cryptic and pseudocryptic diversity of conjugating green algae (Zygnematophyceae)
Kupčíková, Eva ; Šťastný, Jan (advisor) ; Škaloud, Pavel (referee)
This bachelor thesis summarizes the most commonly used species concepts in the class Zygnematophyceae. This group of algae and the molecular markers used in the zygnematophytes' molecular phylogeny will be presented in this thesis. Zygnematophytes have unicellular or multicellular forms and they generally occur in freshwater habitats. Desmids are useful as indicators of water quality and they are also used for scoring of conservation value. Therefore it is important to have the species well defined. The confusion in defining of desmid species was caused by often very variable morphology. Some authors had different opinions on the classifying of desmid species and theirs subunits. The combination of molecular phylogeny, electron microscopy and geometric morphometrics was used in revealing of (pseudo)cryptic species in the genera Micrasterias or Xanthidium. The geometic morphometrics was helpful for finding of important details for distinguishing of particular pseudocryptic species. Key words: cryptic and pseudocryptic diversity, conjugation, desmids, Micrasterias, Euastrum, Xanthidium, molecular phylogeny, taxonomy, geometric morphometrics, biogeography, green algae
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Unveiling hidden species diversity in desmids (Desmidiales, Viridiplantae)
Šťastný, Jan ; Neustupa, Jiří (advisor) ; F.M. Coesel, Peter (referee) ; Kaštovský, Jan (referee)
The delineation of desmid species was traditionally based on purely morphological features. However, a frequent misinterpretation of morphological variability in desmids has led in the past to extensive taxonomical confusion within this important group of green algae which complicates the interpretation of their biodiversity in freshwater ecology, biogeography and biomonitoring. Consequently, I focused in this thesis predominantly on a previously neglected issue, the application of polyphasic approaches in the species-level taxonomy of desmids. In the most studies, a combination of both traditional morphological and modern molecular phylogenetic and geometric morphometric methods has been used to evaluate the taxonomy of selected desmid species, particularly representatives of the morphologically complex genera Micrasterias and Xanthidium. In two papers, I used the combination of traditional morphological and autecological data to clear up the taxonomy of several morphologically less prominent desmid taxa. Generally, the results of the thesis demonstrated that the way we recently see the diversity and distribution of desmids should be thoroughly changed. The real species diversity is mostly distinctly finer than that estimated by classical morphological taxonomy, often corresponds to varieties of...
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Phylogenetic analyses of myxosporeans based on the molecular data
BARTOŠOVÁ, Pavla
This thesis is focused on the assessment of the phylogenetic position of the Myxozoa within the Metazoa, study of the evolutionary relationships within myxosporeans and investigation into the cryptic species assemblages of several myxosporeans based on the ribosomal and protein-coding data. The major part of this work was to confirm the evolutionary trends within myxosporeans based on a single gene by other molecular markers in order to find out if the reconstructed relationships correspond to the real organismal phylogeny. This has been a crucial step for future actions in solving the discrepancies between the myxosporean phylogeny and taxonomy.
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