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Methods of DNA tandem repeats analysis
Havlík, Kryštof ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This work clarifies basics of the repetitive DNA and evaluates thee tandem repeats finders, which are accessible to public free of payment. Second part describes an algorithm used for searching tandem repeats, based on converting DNA string into numerical signal. Then follows signal processing using short-time Fourier transform, formation of spectrogram and analysis for evaluating position and content of repetitive areas. Result of this work is comparison of outcomes provided by public accessible programs with results of created program and review of advantages and disadvantages.
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Reconstruction of Repetitive Elements in DNA
Hypský, Jan ; Martínek, Tomáš (referee) ; Puterová, Janka (advisor)
Eukaryotic genomes contain a large number of repetitive structures. Their detection and assembly today are the main challenges of bioinformatics. This work includes a classification of repetitive DNA and represents an implementation of a novel de novo assembler focusing on searching and constructing LTR retrotransposons and satellite DNA. Assembler accepts on his input short reads (single or pair-end), obtained from next-generation sequencing machines (NGS). This assembler is based on Overlap Layout Consensus approach.
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W chromosomes in Lepidoptera: evolution, diversity and molecular features
HEJNÍČKOVÁ, Martina
Sex chromosome evolution is a fascinating and very dynamic process, which is best to be studied on diverse groups of organisms. Moths and butterflies (Lepidoptera) are known for their species diversity and female heterogamety, which makes them an ideal research model. Most species of Lepidoptera have a WZ/ZZ (female/male) system, although some species lack the W chromosome. The first part of this thesis discusses possible mechanisms and points of its origin in terms of phylogeny. Specifically, it focuses on the lack of W chromosome in the group of bagworms (Psychidae), supporting recent theory about the independent origin of W chromosomes in Lepidoptera. The second part of the thesis provides valuable information about the W chromosome variability and molecular content within the group of loopers (Geometridae). Finally, the third part describes the accumulation of retrotransposons on the W chromosome in Peribatodes rhomboidaria and emphasizes their importance in the process of sex chromosome differentiation.
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Analýza vybraných W obohacených repetic u předivky brslenové \kur{Yponomeuta cagnagella} (Lepidoptera)
PILÍKOVÁ, Aneta
This thesis focuses on the repetitive sequences located in the W chromosome of the spindle ermine moth (Yponomeuta cagnagella) (Lepidoptera). The copy number of the selected repeats was established in male and female genomes from two geographic populations using real-time PCR (qPCR). Fluorescence in situ hybridization (FISH) was used to localize these sequences in female pachytene nuclei. The satellite tandem repeat and the transposon Maverick are present in the W chromosome in high copy numbers. In contrast to previously conducted bioinformatical analyses, the rDNA cluster is probably localized in an autosome in Y. cagnagella. The Maverick transposon was detected in both extensive terminal regions of the W chromosome.
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Sex chromosome evolution in selected taxa of teleost fishes (Teleostei)
Pavlica, Tomáš ; Sember, Alexandr (advisor) ; Kratochvíl, Lukáš (referee)
Teleosts represent more than half of the extant vertebrate species. They show a wide range of mechanisms driving both sex determination and sex differentiation, including nine sex chromosome systems described to date. Teleost sex chromosomes are generally considered as evolutionarily young, therefore they are suitable for an analysis of the early stages of evolution of these unique genomic regions. The aim of the current thesis was to analyze the presence and degree of differentiation of sex chromosomes in two Nothobranchius killifish species and one Bunocephalus banjo catfish representative using conventional and molecular cytogenetic methods. Different populations of N. kadleci and N. furzeri analysed in this thesis shared anXY sex chromosome system. Despite the obvious heteromorphy of their sex chromosomes, comparative genome hybridization (CGH) did not show any region of differentiation. Analysis of synaptonemal complexes by immunostaining coupled with the mapping of 18S rDNA and telomeric repeats using fluorescent in situ hybridization (FISH) showed mainly standard pairing with the contribution of synaptic adjustment. Pachytene spreads of females from one N. furzeri population contained a small supernumerary chromosome which was not present in metaphases of studied somatic cells. Distribution...
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Reconstruction of Repetitive Elements in DNA
Hypský, Jan ; Martínek, Tomáš (referee) ; Puterová, Janka (advisor)
Eukaryotic genomes contain a large number of repetitive structures. Their detection and assembly today are the main challenges of bioinformatics. This work includes a classification of repetitive DNA and represents an implementation of a novel de novo assembler focusing on searching and constructing LTR retrotransposons and satellite DNA. Assembler accepts on his input short reads (single or pair-end), obtained from next-generation sequencing machines (NGS). This assembler is based on Overlap Layout Consensus approach.
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