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Diversity of Blastocystis (Stramenopiles) in reptiles and arthropods
Lorencová, Markéta ; Čepička, Ivan (advisor) ; Jirků, Kateřina (referee)
The genus Blastocystis has recently attracted the attention of scientists, especially parasitologists. Similarly to the related opalines and proteromonads, Blastocystis is anaerobic and lives endobiotically in the intestine of various animals. This organism is also often found in humans, where it is associated with irritable bowel syndrome, though its pathogenic potential remains uncertain. The genus Blastocystis is remarkable for its rich genetic diversity. The taxonomy of Blastocystis is inconsistent and problematic. The strains isolated from homoiothermic vertebrates are divided into 17 subtypes, while strains from poikilotherms are either classified as separate species or are not considered in taxonomic studies at all. The aim of the study was to further examine the genetic diversity of the genus Blastocystis. We determined SSU rDNA sequences of 38 strains isolated from poikilothermic vertebrates and arthropods. The results of our phylogenetic analysis showed that Blastocystis is considerably diverse in these hosts, and we defined 21 new subtypes. The total number of known subtypes of Blastocystis has thus increased to 38. We also examined light-microscopical morphology of some strains. Most of the newly defined subtypes show identical morphology, ST20 (Blastocystis geocheloni) is an exception,...
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The genetic links around the Red Sea as revealed by the mtDNA
Čížková, Martina ; Černý, Viktor (advisor) ; Rídl, Jakub (referee)
The Red Sea region is one of the important places that allow us to uncover traces of the evolution of anatomically modern humans. Besides the questions related to its expansion out of Africa, this region is also important in terms of the mutual influence between populations of Africa and Arabia that after a long period of isolation and genetic differentiation related to climate change in the Pleistocene and subsequent development of seaways and land routes in the Holocene began to contact with each other more frequently. Number of genetic analyzes has been done but some issues concerning on the later development still remain inadequately answered, mainly because of insufficient material. This work is focused on the analysis of 200 mtDNA sequences of four Sudanese populations - two populations of nomadic herdsmen Rashaida and Beja living in the close neighborhood around the city of Kassala and speaking different languages and two populations of the Nile Valley with settled way of life. Analysis of the intrapopulation level revealed much higher diversity of the sedentary populations (in this work the sedentary populations are represented by the Nubians and Arabs). Interpopulation variability and genetic distances within other 46 populations of the Red Sea showed that although Rashaida and Beja people...
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Impact of river system structure on the genetic diversity of reed populations
Fuxová, Gabriela ; Fér, Tomáš (advisor) ; Kubátová, Barbora (referee)
Many plant species are closely related to river biotopes or to biotopes influenced by rivers. River systems create important linear corridors in ecosystems and directly or non-directly influence spatial spread of species in these environments. This offer many questions about species spread in this system. We can answer these questions by using molecular methods. Using 10 microsatellite (SSRs) primers, 202 individuals of Phragmites australis from 60 populations were analysed. Those analyses allowed reveal kinship of individuals, obtain information about spatial spread of populations and about spreading of common reed. Phragmites australis creates both - monoclonal and polyclonal - populations. Dependence of rate of clonality on environment was revealed. Populations from river banks are more monoclonal, populations from pond shores are more polyclonal. Populations are isolated. The highest percentage of variability was explained on among-population level. This is common for anemochoric species. Communication between populations is present, more on shorter distances. Evidence for vegetative spread was found on short distance. Generative spread is much more common. Long-distance spreading is mediated by generative diaspores - seeds. This spreading includes within-river spread, among-river spread and spreading...
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Diversity of the genus Blastocystis (Stramenopiles)
Lorencová, Markéta ; Čepička, Ivan (advisor) ; Kostka, Martin (referee)
Although the genus Blastocystis is only little known, it has recently attracted much attention of protistologists and parasitologists. Similarly to the related opalines and proteromonads, Blastocystis is anaerobic and lives endobiotically in intestines of many animals. On the other hand, members of the genus have completely lost flagella. Therefore, the phylogenetic position of Blastocystis had been puzzling for a long time. B. hominis is one of the most common intestinal parasites of humans and has been found also in a wide variety of animals. It is highly prevalent not only in the developing nations, but also in the developed countries. Its enormous genetic diversity, pathogenic and zoonotic potential (B. hominis is often associated with irritable bowel syndrome) make from B. hominis an important emerging pathogen.
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Mophological and molecular diversity of a tropical tree species Guazuma crinita in the Peruvian Amazon
Tuisima Coral, Lady Laura ; Lojka, Bohdan (advisor) ; Helena, Helena (referee)
Fast growing tree species Guazuma crinita (Malvaceae) was selected as a priority species for domestication in the Peruvian Amazon due its important contribution to the livelihood of local farmers. Its domestication process is still in an early age as for many tropical tree species little is known about its genetic variability and we dont know anything about the impact of domestication on its genetic resources. The main objective of this research was to assess the genetic variability of G. crinita within and among populations in the Peruvian Amazon by the use of morphological (wood physical traits) and molecular (ISSR and AFLP) markers.
Wood physical properties among six G. crinita provenances were evaluated. Wood samples were drilled from the base middle and top of the stem of 12 randomly selected eight-years-old trees for determination of wood measurement. Pearson correlations between physical properties were also determined. All wood physical properties except green density differed significantly among provenances. We also found statistically significant variation due to stem level position. The moderately dense wood and the coefficient of anisotropy (1.6) suggested that G. crinita has stable wood; they represent important advantages in terms of costs for transport and transformation process. The results suggested potential to select provenances with desirable wood properties for further breeding and domestication. Due to the variation found even in limited tree samples it is recommended further analysis with more extensive number of samples from different provenances and planting zones.
This research presents the first assessment of genetic variability based on inter-simple sequence repeat (ISSR) markers for 44 G. crinita genotypes from a clonal garden multiplication established in the Peruvian Amazon Research Institute (IIAP) in Ucayali region. Ten ISSR primers amplified a total of 65 bands of which 61 were polymorphic (93.8%). The range of DNA amplification varied from 260 to 2200 bp. Among the provenances overall genetic differentiation (Gst) was 0.03 indicating 97% of genetic diversity within provenances. Gene flow (Nm) was 12.9 alleles per generation. Cluster analysis was not related with geographic origin suggesting a common gene pool which was supported by calculation of weak positive correlation was found between genetic and geographic distance.
With the use of AFLP markers an insight on how domestication process does impact G. crinita genetic resources is also reported on this research work. I was able to generate fingerprint for 58 leaf samples representing eight provenances and three population types, 19 from a natural regenerated population 15 cultivated in home garden nursery and 24 from a collection of genotypes considered as semi-domesticated population. Seven selective AFLP primer combinations were used. A total of 171 fragments were amplified with 99.42% of polymorphism at species level. Each type of population generated fragments with 72.51% 49.12% and 54.39% of polymorphic fragments respectively. Neis genetic diversity and Shannon index information were found to be higher in the population of natural regeneration compared to overall semi-domesticated population (He = 0.10 and 0.9; I = 0.19 and 0.16 respectively). The analysis of molecular variation (AMOVA) showed higher variation within provenances rather than among (84% and 4% respectively). UPGMA clusters analysis and PCoA did not showed correspondence between genetic and geographic distance in addition their correlation was not significant. There was a significant genetic differentiation among types of population suggesting slight genetic bottleneck in semi-domesticated populations yet with relatively high levels of genetic variation.
In situ conservation for populations with high levels of genetic diversity was recommended. In addition proper management of natural regeneration and ex situ genotype collections might be a good conservation strategy to maintain G. crinita genetic resources.
The use of morphological (wood physical traits) and molecular markers were successful to reveal genetic variability of G. crinita and they could be used for other tropical tree species. For further researches it is emphasis to extent the number of samples and geographic scale.
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Genetic diversity of baobab (&-lt;i&-gt;Adansonia digitata&-lt;/i&-gt; L.) along an elevation transect in Kenya
Chládová, Anna ; Lojka, Bohdan (advisor) ; Petra, Petra (referee)
@Adansonia digitata@L. (Malvaceae) is a huge multipurpose tree of the savannahs of sub-Saharan Africa with high economic potential for local communities. The edible fruits and leaves are known for their high nutritional values and can be used fresh or processed. However, a high intra-specific variability regarding morphology, genetics and nutritional content of baobab and its products is documented for several African regions, while data for Kenya is largely lacking. This study aimed at documenting the genetic and morphological variability of baobab accessions in Kenya and at checking the presence of the newly described diploid baobab species @Adansonia kilima@. Samples were collected from 204 baobab trees from seven populations defined by geographical distance in South-eastern and Coastal Kenya at altitudes of 6-1,058 m asl. Leaf or bark samples for genetic diversity assessment were collected from all 204 trees, while leaves only from 65 and fruits from 76 trees (all in inland locations) for morphological analyses based on the publication Descriptors for Baobab. Nine microsatellite loci were used to assess genetic variation and results analysed with specific software because of the tetraploid nature of baobab. Overall genetic diversity was high and all loci were polymorphic. The mean gene diversity was 0.803 and observed heterozygosity was 0.907. Analysis of molecular variance (AMOVA) revealed low variation among populations (12.4%) and high variation within populations (87.6%). Bayesian clustering and Principal Coordinate Analysis divided the accessions into two clusters, one with only inland and one with coastal accessions. Although the presence of @Adansonia kilima@ was previously postulated for Kenya, flow cytometry did not detect any among the analysed samples as only tetraploids were observed. Regarding morphological characteristics, no differences among the fruit accession from inland populations were found (no fruits were collected in coastal areas). Leaf morphological data showed significant differences between inland and coastal populations with longest leaflets and leaf petioles in accession from the Coast, thus confirming the results obtained for genetic analysis. This study contributes to the overall knowledge of the genetic diversity of baobab in Kenya and can contribute to the development of germplasm conservation strategies and domestication programs for baobab.
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Analýza genetické variability jírovce maďalu pomocí DNA markerů
Bačovský, Václav
Some species of the genus Aesculus are every year heavily infested by horse chestnut leaf miner (Cameraria ohridella), whose larvae are mining the leaves, and under appropriate conditions may damage up to 100% of the leaf area. The effect of lower defense capability of infested trees lead to invasion of fungal (Erysiphe flexuosa, Guignardia aesculi) and bacterial (Pseudomonas syringae pv. aesculi) pathogens, and later to higher mortality of infected individuals. In this study were measured the genetic diversity of species A.hippocastanum, A. turbinata, A. glabra, A. parviflora, A. glabra var. arguta, A. x carnea, A. marilandica, A. pavia, and their genotypes with different susceptibility to the leaf miner. Analysis of 8 microsatellite loci, using the SB buffer for separation, showed high polymorfic information content 0.45 -- 0.77 (0,60 in average) and high genetic diversity. For each loci was found average 5.5 aleles. During two vegetation period, leaf area damage of these genotypes was evaluated in statistical software Assess 2.0. Different pressure of leaf miner and different development at each locality was recorded, and even in some cases lower damage was found, in one case it occured permanently. According to the data obtained, the pathological scale was established and the dendogram of similarity was created. Three groups of resistant, non -- resistant and immune individuals were distinguished and five main section of Aesculus was found. By cloning and analysing the inner transcribed spacers, ITS1 and ITS2, inner and inter species variability was examined. For the sequence of hybrid species A. x carnea no compliance was found in NBCI, therefore first sequence of this genotype was obtained.
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Hodnocení genetické diverzity genových zdrojů rostlin, programy, modely, využití
Oshea, Denisa
The bachelor thesis is a literature review on the topic of genetic diversity evaluation. The beginning is devoted to genetic diversity in general terms, its importance, its history, and its loss, that is irrecoverable and is regarded by many as the most important environmental problem. In addition, its protection, which is very important and in the Czech Republic is secured by the National program for conservation and utilization of plant genetic resources. The work also describes the methods of evaluation from morphological, through biochemical to molecular. There are described and compared mainly molecular methods such as RAPD, AFLP, RT-PCR, and others. The last part is devoted to a description of some plant genomes databases. One of them is for example The European Vitis Database.
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Methodical aspects of genetic diversity of cattle
MIJAILOVIĆ, Angelina
The aim of this thesis is to describe methods for assessing genetic diversity. At the beginning is described biological diversity and its distribution with focus on genetic diversity. Furthermore, mutations, segregation, recombination, migration, selection, genetic drift, and inbreeding are described. The work also deals with the polymorphisms including SNP, VNTR and microsatellites. They are described as genetic markers, marker assisted selection and genomic selection. For within-population genetic diversity the text deals with biometric methods, the part describing interpopulation genetic diversity is concerned to distances and software packages. Finally, the phylogenetic trees and thein types are described with examples of use in practice.
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Chosen problems of genetic diversity of dog
CHLUPATÁ, Lucie
The bachelor thesis is worked out in the form of the research on the theme "Selected questions from the genetic diversity of dogs". The aim of this work was processing of the current situation of scientific knowledge in the field of genetic diversity of dogs. Firstly, the origin is described in the thesis, domestication of dogs, an organisation dealing with dogs breeding and selected breeds of dogs. From the genetic site point of view, the basic terms in genetics are described genetic markers, DNA profile of dog and the methods of evaluation of genetic diversity. In the end of my bachelor thesis I outlined possible recommendations for dog breeders.
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