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Current genomic and cytogenomic methods in analysis of chromosome rearrangements
Buryšová, Sára ; Sember, Alexandr (advisor) ; Mandáková, Terezie (referee)
Chromosome rearrangements represent one of the major mechanisms driving the eukaryotic genome evolution. They may significantly contribute to reproductive isolation and diversification, including the evolution of complex life-history traits linked e.g. with local adaptation. They are structural changes leading to alteration in the morphology and/or number of chromosomes, which can have a direct effect on the evolution of genes and their expression profiles, the frequency and distribution of recombination in the genome, and the functional dynamics of processes operating in the interphase nucleus. However, they may be also causal for etiology (or a consequence) of inherent diseases and tumorigenesis. The study of chromosome rearrangements and the mechanisms of their emergence is related to the identification and characterization of rearrangement breakpoints (i.e. where double-strand break occurred and chromosome segments subsequently rejoined). One possibility is to analyze chromosomes and interspecific changes in the arrangement of linkage groups/synteny blocks using cytogenetic and cytogenomic methods (e.g. cross-species mapping of whole-chromosome hybridization probes). More detailed insight is provided by comparative genomics, nowadays mainly represented by so-called third-generation methods (the...
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Chromosomal collinearity and karyotype evolution in crucifers (Brassicaceae)
Mandáková, Terezie
The Brassicaceae (Crucifereae) comprises 49 tribes, 321 genera and 3660 species, and belongs to the largest plant families. Whole-genome sequencing of the model plant Arabidopsis thaliana fuelled the interest of scientists in the mustard family as well as rapid development of comparative phylogenomics and cytogenomics, including the invent of chromosome painting in A. thaliana and comparative chromosome painting (CCP) in other Brassicaceae species. The Brassicaceae is the only plant family in which large-scale CCP is feasible. CCP provides unique insights into the karyotype and genome evolution in plants by comparing chromosome collinearity, identification of chromosome rearrangements, construction of comparative cytogenetic maps, and reconstruction of ancestral karyotype structures. This PhD thesis deals with the karyotype evolution in the Brassicaceae family uncovered by comparative chromosome painting. The introductory part is divided into four chapters. The first chapter introduces chromosomes, karyotypes, karyotypic variation, and the role of chromosome rearrangements and polyploidy in the karyotype and genome evolution. In the methodical second part, principles of chromosome painting are described. The core third chapter focuses on comparative cytogenomics in the Brassicaceae, and summerizes...
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Chromosomal collinearity and karyotype evolution in crucifers (Brassicaceae)
Mandáková, Terezie
The Brassicaceae (Crucifereae) comprises 49 tribes, 321 genera and 3660 species, and belongs to the largest plant families. Whole-genome sequencing of the model plant Arabidopsis thaliana fuelled the interest of scientists in the mustard family as well as rapid development of comparative phylogenomics and cytogenomics, including the invent of chromosome painting in A. thaliana and comparative chromosome painting (CCP) in other Brassicaceae species. The Brassicaceae is the only plant family in which large-scale CCP is feasible. CCP provides unique insights into the karyotype and genome evolution in plants by comparing chromosome collinearity, identification of chromosome rearrangements, construction of comparative cytogenetic maps, and reconstruction of ancestral karyotype structures. This PhD thesis deals with the karyotype evolution in the Brassicaceae family uncovered by comparative chromosome painting. The introductory part is divided into four chapters. The first chapter introduces chromosomes, karyotypes, karyotypic variation, and the role of chromosome rearrangements and polyploidy in the karyotype and genome evolution. In the methodical second part, principles of chromosome painting are described. The core third chapter focuses on comparative cytogenomics in the Brassicaceae, and summerizes...
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