|
|
Phylogenetic analysis and molecular detection of coronaviruses
MARHOUNOVÁ, Lucie
The aim of this bachelor thesis was to get acquainted with the creation of phylogenetic trees, which describe the relationships between coronaviruses and compare and assess the suitability of used and designed primers for the detection of a new type of coronavirus SARS-CoV-2. According to phylogenetic trees, it is possible to determine the evolutionary relationship of the studied organisms, which during evolution are subject to changes in their sequences, so-called mutations. These changes determine their development. The theoretical part of the bachelor thesis was focused on general acquaintance with viruses and subsequently coronaviruses and a new type of coronavirus SARS-CoV-2. SARS-CoV-2 has posed and continues to pose a major threat to the world. Furthermore, the issue of phylogenetics and finally the PCR detection method were discussed. In the practical part, phylogenetic trees were created using the computer program MEGA-X using the Neighbor-Joining method, which examined the phylogenetic relationships between coronaviruses focused mainly on SARS-CoV-2. The nearest coronaviruses of this new type of SARS-CoV-2 coronavirus were further compared using special BLAST software, which reported the percent agreement of the studied sequences. During these analyzes, SARS-CoV-2 was found to be most like the bat coronavirus RaTG13. Primers that are commonly used to detect SARS-CoV-2 are not disclosed, therefore primers from the CoVrimer web application have been used, where primers that have been used for scientific research are available. These were compared with the primers designed by the author. The design was performed as part of a bachelor's thesis using a special application Pirmer-BLAST. The primers obtained from the CoVrimer application were not designed to comprehensively distinguish all SARS-CoV-2 variants studied.
|
|
|
Fylogeneze a taxonomie vybraných druhů sinic čeledi Merismopediaceae s využitím metody single cell sequencing
POKORNÝ, Jan
Thanks to new molecular methods, which have been used for revision of many traditional cyanobacterial taxa, their real systematic positions have become clearer. Merismopediaceae is a relatively understudied group of Cyanobacteria, therefore many subordinate taxa have not been sufficiently molecularly reviewed. In this thesis standard molecular methods of the polyphasic approach were used on environmental isolates as well as cultured strains of Merismopediaceae taxa. Subsequent phylogeny analysis based on 16S rRNA gene shows the polyplyly of genera Merismopedia and Eucapsis. The thesis also includes the very first molecular evidence of the taxonomic position of the genus Microcrocis.
|
|
| |
|
|
World travellers: phylogeny and biogeography of the butterfly genus Leptotes (Lepidoptera: Lycaenidae)
PAPP MAREŠOVÁ, Jana
In this thesis, we investigated phylogenetic and biogeographical relationships of neglected butterflies of the subtribe Leptotina (Lepidoptera: Lycaenidae), widely distributed in tropical and subtropical areas around the world. We used both mitochondrial and nuclear markers and different molecular analyses to resolve relationships within the subtribe. We also focused on diversification times and biogeographical patterns of Old World taxa and detailed phylogeography of the most widespread species, Leptotes pirithous.
|
|
| |
|
| |
|
|
Fylogeografie komplexu \kur{Phasianus colchicus}
KOFRÁNEK, Zdeněk
Rod Phasianus se v současné době dělí do 2 druhů a 33 poddruhů, které obývají široký areál, táhnoucí se od Japonských Ostrovů až k pohoří Kavkaz. Tato studie měl pracovala s fenotypovými charakteristikami rodu Phasinus za účelem jeho Evoluce. Získané výsledky byly srovnány s dostupnými molekulárními studiemi, zaměřenými na tu samou skupinu .Ve výsledku se ukázalo ,že fenotypové charakteristiky tohoto rodu nám nabízí dostatečné množství fylogeneticky informativních znaků, které dobře korelují s jeho fylogenetickými vztahy
|
|
|
Let's meet in the littoral: Diversity of symbiosis in the Verrucariaceae lichens
Schmidtová, Jana ; Škaloud, Pavel (advisor) ; Peksa, Ondřej (referee)
Lichens are organisms formed by several symbiotic partners, most importantly a fungus (mycobiont) and an alga or cyanobacteria (photobiont). Although most lichens are terrestrial, some can be found also in aquatic environments. Black crustose lichens from the family Verrucariaceae (Verrucariales, Eurotiomycetes, Ascomycota) were able to adapt to this environment very well and often dominate in the seashore near fluctuating water level. The ability of these lichens to inhabit various environments is associated with their unusually wide range of photobionts. However, this symbiont is not known to most of them. This work investigates the diversity of lichens of the family Verrucariaceae in the littoral zone of the Baltic and the North Sea coasts, the relationships between symbionts and the connection between lichen diversity and the salinity gradient. Using metabarcoding, the diversity of free-living algae in the vicinity of the studied lichens is determined and the symbiotic algae are compared with the photobionts found in the lichens. Mycobionts and photobionts were identified using ITS and 18S rDNA. A total of nine lineages of mycobionts and photobionts were found. The most common lichen turned out to be the species Hydropunctaria maura with its photobiont Pseudendoclonium submarinum. For several...
|
|
|
The phylogeny of the Protaetia Burmeister, 1842 flower beetles in the western palearctic region
Žďárská, Kateřina ; Šípek, Petr (advisor) ; Bezděk, Aleš (referee)
This diploma thesis deals with the phylogeny and phylogeography of flower beetles of the genus Protaetia, especially with the complicated taxonomic complex around the species Protaetia (Potosia) cuprea, P. cuprina and P. caucasica in the western Palearctic region. In light of the results presented by Vondráček et al. (2018), it seems that the classic taxonomic approach, based only on coloration, geographical distribution or poorly analysed morphological characters, is not able to adequately explain the evolution of the taxon, nor correctly identify individual taxa at the species level (i.e. species and subspecies). To understand the evolution of the group and the population structure, it is therefore necessary to use the now standard molecular-phylogenetic approaches as well. Based on analyses of one nuclear (internal transcribed spacer 1) and two mitochondrial genes (cytochrome oxidase I and cytochrome b) from 231 individuals, a phylogenetic hypothesis of the West Palaearctic representatives of the genus Protaetia was compiled. It was found that the currently recognized subgenera of the genus do not correspond to the results of the analyses. The subgenera Eupotosia, Netocia and Potosia proved to be non- monophyletic. Within the species complex of P. cuprea, in addition to the European clade of P....
|
|
|
Diversity of the geotrupide genus Jekelius (Coleoptera: Geotrupidae)
Sommer, David ; Král, David (advisor) ; Bezděk, Aleš (referee)
The first part of this thesis focuses on the family Geotrupidae, with special focus on the representatives of the genus Jekelius. It summarizes the present and historical taxonomic concepts and phylogenetic relationships within this family. Moreover, the morphology of adults and larvae and the geographical distribution of individual taxa are described. In the section on the biology and ecology of the family, emphasis is placed especially on feeding strategies, breeding behaviour and parental care. The results of this thesis consist of three parts, 1) taxonomy, 2) molecular analyses, and 3) flow cytometry. The first part brings a taxonomic revision of the Jekelius brullei species complex defined here. This part focuses on redescribing each known species, as well as describing additional species not yet formally described. This thesis defines the distribution ranges of each species based on previously published literature and our own data. Molecular analyses performed in this thesis generated a phylogenetic tree including a significant part of the species of the Jekelius brullei species complex. The last part of the thesis presents results obtained by flow cytometry for representatives of the species complex Jekelius brullei and a number of other taxa of the family Geotrupidae. The discussion then...
|
guest ::
