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Evolution and genomics of symbionts in Hippoboscidae
ŠOCHOVÁ, Eva
Obligately blood-sucking parasites harbour symbiotic bacteria providing them B-vitamins and cofactors missing from their blood diet. Within Hippoboscoidea group (parasites of birds and mammals), tsetse flies as medically important vectors have been studied extensively while bat flies and louse flies tend to be neglected. This thesis is composed of two complementary manuscripts focused on phylogeny and origin of bacterial symbionts in Hippoboscidae family (manuscript 1) and their genome evolution (manuscript 2). First, phylogenetic approach was employed to determine lineages of obligate and facultative symbionts present in this group. Second, genomic and phylogenomic analyses were carried out to better understand evolution of obligate endosymbionts from the Arsenophonus genus in this group. Results of the two studies indicate that relationships between Hippoboscoidea and their symbionts are extremely dynamic with frequent replacements of obligate symbionts. This hypothesis is supported by both phylogenetic and genomic evidence, in particular, Arsenophonus endosymbionts of Hippoboscidae represent several distinct lineages (of likely different ages) with noticeable differences in genome features and metabolic capabilities. The data presented in this thesis thus greatly extend our knowledge about evolution and genomics of symbiotic bacteria in Hippoboscidae and bloodsucking hosts in general.
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Identification of Organisms Based on Analysis of Nucleotide Density Vectors
Maděránková, Denisa ; Babula, Petr (referee) ; Schwarz, Daniel (referee) ; Provazník, Ivo (advisor)
Most methods for analysis of genomic data work with symbolic sequences. Numerically represented genomic sequences can be analyzed by signal processing methods. A new method of numerical representation of DNA sequences, nucleotide density vectors, is proposed in this thesis. Usability of this method for purposes of molecular species identification is tested on DNA barcoding sequences. DNA barcoding is modern and popular methodology based on comparison of short mitochondrial DNA sequences. Beside species identification by proposed method based on nucleotide density vectors, higher taxa rank identification (e.g. families) was also tested. Furthermore, dendrograms were constructed from standardly used evolutionary distances and distances between nucleotide density vectors and the dendrograms were compared.
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