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Physical mapping of genome regions without linkage map using BAC clones in Xenopus tropicalis
Špirhanzlová, Petra ; Krylov, Vladimír (advisor) ; Marec, František (referee)
Xenopus leavis was a favorite model organism during the 20th. century, but nowadays it has been replaced by diploid Xenopus tropicalis, which has not only shorter generation time, but also smaller genom. One of the disadvantages of Xenopus tropicalis is the lack of full physical and linkage map. According to JGI genome database (assembly 4.1) there are unmapped regions on short arm of the chromosome 2 and 7 . Several BAC clones ( with a single or dual-end sequence) has been found to be located within this region, according to a recent assembly 7.1. However , it isn't clear whether 100bp length of BAC ends is enough to place entire BAC clone into the genom of Xenopus tropicalis. In order to prove correct inclusion of these BAC clones into JGI database, several BAC clones, which are supposed to be located on short arm of chromosome 2, were picked. Using fluorescence in situ hybridisation, the signal of these BAC clones was localised on the short arm of chromosome 1 instead of chromosome 2 and in most cases they had opposite orientation. It means that the 100bp lenght of BAC ends propably isn't sufficient to place entire BAC clone on chromosome. New working protocol of BAC DNA isolation and labeling was established.
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Insights into the karyotype evolution of pseudoscorpions (Arachnida:Pseodoscorpiones)
Šťáhlavský, František ; Smrž, Jaroslav (advisor) ; Marec, František (referee) ; Ráb, Petr (referee)
6. ZÁVĚRY 1. Pro studium karyotypu štírků je u většiny druhů nejvhodnější doba rozmnožování. Ve střední Evropě se dá v tomto období (duben - červen) u většiny druhů získat z gonád samců i samic dostačující množství spermatogoniálních mitóz a u samců i různá meiotická stadia vhodná pro analýzu karyotypu. 2. Primární konstrikce řady druhů jsou drobné a obtížně detekovatelné. Pro přesné vyhodnocení morfologie chromosomů jsou proto daleko vhodnější metafáze II samců. V této fázy jsou chromatidy chromosomů spojeny pouze v oblasti centromer, poloha primárních konstrikcí se tedy dá přesně stanovit. 3. Štírci jsou charakterističtí velkou mezidruhovou variabilitou v počtu a morfologii chromosomů. Diploidní počet chromosomů se v rámci celého řádu pohybuje od 7 až po 137. Nejnižší počty chromosomů má čeleď Olpiidae (2n=7-23), nízké počty chromosmů mají také čeledi Chthoniidae (2n=10-38), Geogarypidae (2n=15-23) a Garypinidae (2n=33). Nejvyšší počty chromosomů má čeleď Atemnidae (2n=93-137). 4. Původním systémem chromosomového určení pohlaví štírků je patrně X0. S výjimkou čeledi Larcidae byl tento systém nalezen u všech studovaných čeledí. V rámci čeledí Neobisiidae a Larcidae byl zjištěn také systém XY, jež vzniká pravděpodobně přestavbami mezi chromosomem X a autosomy. 5. Pohlavní chromosom se v průběhu meiosy...
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Genetic mapping in Xenopus
Seifertová, Eva ; Krylov, Vladimír (advisor) ; Ráb, Petr (referee) ; Marec, František (referee)
The diploid amphibian Xenopus tropicalis represents a significant model organism for studies of early development, genes function and evolution. Such techniques as gynogenesis, injection of morpholino antisense oligonucleotide into fertilized eggs or transgenesis were established. In the recent ten years, many efforts have been made to complete the sequence information. X. tropicalis genome has been sequenced but the completion of its assembly only on the basis of sequence data has been impossible. Therefore, our first work was focused on one of approaches for a genome completing- genetic mapping. First of all, the genetic map of Xenopus tropicalis was established pursuant linkage and physical positions of markers. Since the map contained gaps, we developed a new method for genetic mapping based on the next generation sequencing of laser microdissected arm. Using Illumina next generation sequencing of fifteen copies of a short arm of chromosome 7, we obtained new insights into its genome by localizing previously unmapped genes and scaffolds as well as recognizing mislocalized portions of the genome assembly. This was the first time laser microdissection and sequencing of specific chromosomal regions has been used for the purpose of genome mapping. These data were also used in the evolution study of...
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Mechanisms of the karyotype evolution in scorpions (Arachnida: Scorpiones)
Štundlová, Jana ; Šťáhlavský, František (advisor) ; Špakulová, Marta (referee) ; Marec, František (referee)
Scorpions represent an ancient group of arachnids that have colonized a diverse range of terrestrial environments since Silurian times. Despite their long evolutionary history and ecological diversity, these animals are characterized by morphological stasis. However, the uniform morphology of extant scorpions may hide the true diversity of contemporary lineages. The study of cytogenetic traits thus has the potential to deepen our knowledge of the diversity of contemporary scorpion taxa and bring new insight into the processes underlying karyotypic changes in this group of arachnids. The subject of this thesis is to examine the diversity and dynamics of karyotypes of selected scorpion groups with holokinetic and monocentric chromosomes. Comparative cytogenetic analysis, including more than 110 species from five families, was based on standard cytogenetic techniques and mapping of the gene for 18S ribosomal RNA and telomeric (TTAGG)n repeats by fluorescence in situ hybridization (FISH). To elucidate the fundamental structural mechanisms underlying karyotype differentiation in the studied groups, the emphasis was placed on the interconnection of cytogenetic and sequence data of the analyzed species. The knowledge of the genetic structure and phylogenetic relationships of studied taxa played a crucial...
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Mechanisms of the karyotype evolution in scorpions (Arachnida: Scorpiones)
Štundlová, Jana ; Šťáhlavský, František (advisor) ; Špakulová, Marta (referee) ; Marec, František (referee)
Scorpions represent an ancient group of arachnids that have colonized a diverse range of terrestrial environments since Silurian times. Despite their long evolutionary history and ecological diversity, these animals are characterized by morphological stasis. However, the uniform morphology of extant scorpions may hide the true diversity of contemporary lineages. The study of cytogenetic traits thus has the potential to deepen our knowledge of the diversity of contemporary scorpion taxa and bring new insight into the processes underlying karyotypic changes in this group of arachnids. The subject of this thesis is to examine the diversity and dynamics of karyotypes of selected scorpion groups with holokinetic and monocentric chromosomes. Comparative cytogenetic analysis, including more than 110 species from five families, was based on standard cytogenetic techniques and mapping of the gene for 18S ribosomal RNA and telomeric (TTAGG)n repeats by fluorescence in situ hybridization (FISH). To elucidate the fundamental structural mechanisms underlying karyotype differentiation in the studied groups, the emphasis was placed on the interconnection of cytogenetic and sequence data of the analyzed species. The knowledge of the genetic structure and phylogenetic relationships of studied taxa played a crucial...
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Insights into the karyotype evolution of pseudoscorpions (Arachnida:Pseodoscorpiones)
Šťáhlavský, František ; Smrž, Jaroslav (advisor) ; Marec, František (referee) ; Ráb, Petr (referee)
6. ZÁVĚRY 1. Pro studium karyotypu štírků je u většiny druhů nejvhodnější doba rozmnožování. Ve střední Evropě se dá v tomto období (duben - červen) u většiny druhů získat z gonád samců i samic dostačující množství spermatogoniálních mitóz a u samců i různá meiotická stadia vhodná pro analýzu karyotypu. 2. Primární konstrikce řady druhů jsou drobné a obtížně detekovatelné. Pro přesné vyhodnocení morfologie chromosomů jsou proto daleko vhodnější metafáze II samců. V této fázy jsou chromatidy chromosomů spojeny pouze v oblasti centromer, poloha primárních konstrikcí se tedy dá přesně stanovit. 3. Štírci jsou charakterističtí velkou mezidruhovou variabilitou v počtu a morfologii chromosomů. Diploidní počet chromosomů se v rámci celého řádu pohybuje od 7 až po 137. Nejnižší počty chromosomů má čeleď Olpiidae (2n=7-23), nízké počty chromosmů mají také čeledi Chthoniidae (2n=10-38), Geogarypidae (2n=15-23) a Garypinidae (2n=33). Nejvyšší počty chromosomů má čeleď Atemnidae (2n=93-137). 4. Původním systémem chromosomového určení pohlaví štírků je patrně X0. S výjimkou čeledi Larcidae byl tento systém nalezen u všech studovaných čeledí. V rámci čeledí Neobisiidae a Larcidae byl zjištěn také systém XY, jež vzniká pravděpodobně přestavbami mezi chromosomem X a autosomy. 5. Pohlavní chromosom se v průběhu meiosy...
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Cytogenetics of selected groups of ray-finned fishes (Actinopterygii): Evolutionary-ecological questions associated with the dynamics of repetitive sequences and the occurrence of polyploidy
Sember, Alexandr ; Ráb, Petr (advisor) ; Marec, František (referee) ; Král, Jiří (referee)
Ray-finned fishes (Actinopterygii) exhibit the greatest biodiversity among vertebrates. The vast majority of extant actinopterygian fish species belong to clade Teleostei - a lineage whose significant evolutionary success might have resulted from a teleost specific whole- genome duplication (TSGD) that occurred at the onset of this group, subsequent to its divergence from the rest of actinopterygian lineages. Despite the growing body of sequenced fish genomes and analyses of their transcriptomes, the largest contribution to understanding fish genomes comes from analyses of DNA content and from cytogenetics. Genomes of ray-finned fishes and especially those of Teleostei exhibit vast diversity and rapid dynamics of repetitive DNA sequences whose variability is reflected in a wide range of fish genome sizes and in the dynamics behind karyotype differentiation. Therefore, ray-finned fishes offer a unique opportunity to study genome variability as a driving force underlying morphological and ecological diversification, evolution and adaptation. Particularly, the mapping of repetitive DNA sequences by means of fluorescence in situ hybridization (FISH) has proven to be a very useful and informative approach during the last two decades and contributed greatly to our understanding of the fish genome...
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Genetic mapping in Xenopus
Seifertová, Eva ; Krylov, Vladimír (advisor) ; Ráb, Petr (referee) ; Marec, František (referee)
The diploid amphibian Xenopus tropicalis represents a significant model organism for studies of early development, genes function and evolution. Such techniques as gynogenesis, injection of morpholino antisense oligonucleotide into fertilized eggs or transgenesis were established. In the recent ten years, many efforts have been made to complete the sequence information. X. tropicalis genome has been sequenced but the completion of its assembly only on the basis of sequence data has been impossible. Therefore, our first work was focused on one of approaches for a genome completing- genetic mapping. First of all, the genetic map of Xenopus tropicalis was established pursuant linkage and physical positions of markers. Since the map contained gaps, we developed a new method for genetic mapping based on the next generation sequencing of laser microdissected arm. Using Illumina next generation sequencing of fifteen copies of a short arm of chromosome 7, we obtained new insights into its genome by localizing previously unmapped genes and scaffolds as well as recognizing mislocalized portions of the genome assembly. This was the first time laser microdissection and sequencing of specific chromosomal regions has been used for the purpose of genome mapping. These data were also used in the evolution study of...
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Evolution of selected karyotype characters in tetrapulmonate arachnids
Jílková, Klára ; Král, Jiří (advisor) ; Marec, František (referee)
The class Arachnida is not thoroughly explored from the cytogenetic point of view. Previous studies suggest a high diversity of karyotypes and sex determination in arachnids. This study deals with the evolution of sex chomosomes, nucleolar organizer regions (NOR), and telomeric repeats in the tetrapulmonate clade of arachnids, particularly in groups of ancient origin. Sex chromosomes were detected in two orders. Detection of NORs in a large set of species supports the hypothesis that the ancestral karyotype of arachnids contained NOR on one pair of autosomes only. The number of NORs has increased during the evolution of some groups of Pedipalpi. The NORs are located in terminal or subterminal chromosomal regions in most tetrapulmonates. The occurrence of the "insect" telomeric motif was confirmed in majority of tetrapulmonates. Interstitital telomeric repeats were not detected with the exception of one species. Keywords: arachnids, meiosis, sex chromosomes, telomeres, nucleolar organizer, heterochromatin
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