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Genome size estimation in protists
Lukeš, Jiří ; Čertnerová, Dora (advisor) ; Veselská, Tereza (referee)
This bachelor's thesis presents the current knowledge of the size of the genome in protists with a focus on the description and comparison of individual methods that were used to solve this issue. Genome size is a characteristic trait of all living organisms and other physiological features related to genome size are also mentioned. Of the selected methods, the greatest emphasis is placed on the flow cytometry, which is considered reliable and currently provides the most data on the size of protist genomes. In addition to flow cytometry, the contribution of whole genome sequencing to understanding the size of protist genomes is mentioned. Problems with estimating the size of protist genomes results from the heterogeneity of protists as a study group and from the non-uniform procedures within individual methods, which make possible comparisons difficult. Protists are evaluated in the work as an insufficiently studied group, within which the size of the genome varies by approximately 200,000×. The conclusion of the thesis summarizes the current knowledge about the genome size of relatively studied groups of protists. Key Words: Genome size, C-value, Protists, Flow cytometry, whole-genome sequencing, pulsed field gel electrophoresis, Feulgen densitometry, microspectrophotometry
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Genome size studies in plants - from intraspecific variation to ecological consequences
Lučanová, Magdalena
Nuclear DNA content (genome size) is one of the basic characteristics of living organisms. In the Angiosperms, the range of genome size is 2,300-fold, which raises questions about the causes and consequences of this tremendous variation. This thesis deals with genome size in plants from the level of intraspecific homoploid variation, through intraspecific ploidy variation, to interspecies comparisons. On various study systems we investigated the dynamics and ranges of genome size variation, tried to reveal possible associations between genome size and selected biological traits, and assessed the extent to which differences in genome size are manifested at the ecological and evolutionary level. As a means of estimating genome size we applied flow cytometry (FCM). In Taraxacum stenocephalum we conducted a detailed study of its enormous genome size variation. We carried out crossings of parents with various genome sizes and compared these parental genome sizes with those of F1 offspring. We also attempted to reveal the association of genome size with various growth traits. In Galium valdepilosum and Arabidopsis arenosa we carried out an extensive flow-cytometric ploidy level screening and compared the distribution and ecological preferences of detected cytotypes. We studied the Andean genus...
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Genome size studies in plants - from intraspecific variation to ecological consequences
Lučanová, Magdalena ; Trávníček, Pavel (advisor) ; Leitch, Ilia (referee) ; Šmarda, Petr (referee)
Nuclear DNA content (genome size) is one of the basic characteristics of living organisms. In the Angiosperms, the range of genome size is 2,300-fold, which raises questions about the causes and consequences of this tremendous variation. This thesis deals with genome size in plants from the level of intraspecific homoploid variation, through intraspecific ploidy variation, to interspecies comparisons. On various study systems we investigated the dynamics and ranges of genome size variation, tried to reveal possible associations between genome size and selected biological traits, and assessed the extent to which differences in genome size are manifested at the ecological and evolutionary level. As a means of estimating genome size we applied flow cytometry (FCM). In Taraxacum stenocephalum we conducted a detailed study of its enormous genome size variation. We carried out crossings of parents with various genome sizes and compared these parental genome sizes with those of F1 offspring. We also attempted to reveal the association of genome size with various growth traits. In Galium valdepilosum and Arabidopsis arenosa we carried out an extensive flow-cytometric ploidy level screening and compared the distribution and ecological preferences of detected cytotypes. We studied the Andean genus...
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Lichen ecology in the relationship to functional diversity and genome size
Konečná, Eliška ; Malíček, Jiří (advisor) ; Palice, Zdeněk (referee)
Eliška Konečná Lichen ecology in the relationship to functional diversity and genome size Abstract This bachelor thesis in its first part summarises and characterizes lichen functional traits and sums up known relation between particular traits and ecological factors of the enviroment. Second part of the thesis focuses on question of genome measurment in general and than summarises known information about lichen genom size. In the second part there is partial focus on relation between genom size and ekology of organisms as well, which could become focus of some study in the future. Key words: functional traits, lichens, mycobiont, genome size
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Orchids as a model for research in ecophysiological adaptations of mycoheterotropic plants
Ponert, Jan ; Lipavská, Helena (advisor) ; Gryndler, Milan (referee) ; Chrtek, Jindřich (referee)
Perhaps all orchids are mycotrophic at early developmental stages, while majority of species photosynthesize at adulthood and only about 200 species remain fully mycotrophic for the whole life. Mycotrophy affects orchids at many levels. In this thesis, I focus on four aspects of orchid biology, which could be connected with mycotrophy: (i) systematics, (ii) genome size and endoreduplication, (iii) regulation of seed germination and (iv) mechanism of transfer of carbon and energy from fungi to orchids. There are over 27,000 recently recognized orchid species, nevertheless new ones are still discovering and old ones are revisiting. In this work I present a description of new species, Cleisostoma yersinii, and its morphological, anatomical, ecological and systematic characterization. Phylogeny reconstruction confirmed relationship with C. birmanicum. In the subtribe Podochileae, I reappraised the genus Campanulorchis to establish monophyletic but also morphologically defined group. For both abovementioned genera I prepared the artificial identification key. In the genus Dactylorhiza I revised taxa present in our country and I prepared an identification key which firstly mentions D. maculata subsp. elodes from Czech Republic. Orchid species diversity is probably reflected in genome structure. Results...
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Introgressive zone of Arabidopsis lyrata and A. arenosa in Central Europe
Hojka, Jakub ; Marhold, Karol (advisor) ; Španiel, Stanislav (referee)
Genetic composition of hybrid zones often reflects geographical and ecological gradients. Hybrid zone of Arabidopsis lyrata and A. arenosa in Central Europe can be convenient model system for testing such hypothesis. These are well circumscribed but still interfertile, and their offspring is fully fertile. Besides repeated hybridisation events, the current state is complicated by the autopolyploidisation events of one of the parents, namely A. lyrata, which is present in the area studied both as diploid and tetraploid. This hybrid zone was already described in previous publications, which showed certain gradient of introgression. Moreover, the area of the hybrid zone represents a transition between Alpine and Pannonian climate along an altitudinal gradient leading from the Prealps to the lowland Wienerwald. The current thesis is the as yet most detailed study of this hybrid zone both in respect of number of studied populations and the amount of data acquired using the methods of RAD Sequencing, multivariate morphometrics and flow cytometry. The analysis of genetic data showed a gradient of introgression, where parental populations are placed at opposite ends, whereas genetically intermediate hybrids are placed in its centre. Analysis of the genome size showed an additional gradient, where hybrids...
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Flow cytometry and its use for study of insects
Stuchlíková, Magdalena ; Janšta, Petr (advisor) ; Sadílek, David (referee)
Flow cytometry is a modern technique in research, playing a significant role in biomedicine and botanics. Despite its benefits (speed, simplicity, low costs), flow cytometry is currently not used in the study of insects on a large scale. This thesis gives an overview as to how flow cytometry is used in research on insects and summarises the results of such study. This pertains to genome size and its connections to other phenomena. Other focal points of research, such as ploidy and base pair ratios, are addressed to a lesser extent. Key words: flow cytometry, use in study of insects, genome size, ploidy, invertebrates
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An assessment of interspecific hybridization between Central-European taxa from the genus Nymphaea: insights from flow cytometry and multivariate morphometrics
Kabátová, Klára
Although the genus Nymphaea (waterlily) includes only two native species (N. alba and allopolyploid N. candida) in Central Europe, it poses a great challenge to taxonomy and biosystematics. The determination of both species is hampered by their phenotypic similarities, and species boundaries can be further blurred by interspecific hybridization. In addition, ornamental cultivars of different parentage that often escape (either accidentally or intentionally) from cultivation and can cross with the native ones make the situation even more complex. To get insight into the caryological and phenotypic variability of czech waterlilies, we used DNA flow cytometry and both distance-based and geometric morphometrics. Collections from natural sites showed two different groups of fluorescence intensities, corresponding to N. alba and N. candida, respectively. In addition, intermediate values of nuclear DNA amount were found in some plants from South Bohemia, indicating their hybrid origin. Morphologically, these plants were partly intermediate between the native species, partly having their separate tendency to oversized growth. Surprisingly, ornamental cultivars (obtained either from commercial stocks or as escapes from the field) possessed the smallest genome sizes. The amount of nuclear DNA therefore seems...
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Genome size evolution in Costaceae
Böhmová, Alžběta ; Fér, Tomáš (advisor) ; Rybka, Vlastimil (referee)
Genome size in plants varies greatly; in angiosperms this variability can make a 2400- fold difference. This is why the subject of many studies is the attempt to explain these differences in various contexts. One of these is the phylogenetic viewpoint, which studies the relationships between genome size and different taxonomic groups. Many studies have been published so far which explore the plants of the temperate zone; there are however very few studies investigating genome size in tropical plants. For this reason, the subject of this thesis is the analysis of genome size in the pantropical family Costaceae Nakai. This family presently includes seven genera: Monocostus K.Schum., Dimerocostus Kuntze, Costus L., Paracostus C.D.Specht, Chamaecostus C.D.Specht & D.W.Stev, Hellenia Retz. and Tapeinochilos Miq., counting altogether about 300 species. The family is sister to the family Zingiberaceae, which has been notably better explored due to its economic importance. One of the aims of this thesis was a partial revision of the phylogeny published by Specht (2006). Molecular methods were used to analyse the phylogenetic relationships; these methods included classical sequencing of the trnL-F region and next-generation sequencing, where probes designed in advance were used to obtain the targeted genes....
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