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Construction and quality assessment of the genome assemblies
Korená, Lucie ; Leontovyč, Roman (advisor) ; Vorel, Jiří (referee)
Detailed information of the genome of the studied organism is crucial for many fields of modern research. Actual sequencing technologies are not able to read the whole DNA molecule at once therefore only fragments of the genetic information are obtained, which are not sufficiently informative on their own. The goal of the genomic-bioinformatic approach is to assemble these fragments into complete original information - genome assembly. The process of the genome assembly is demanding in terms of computational power, software equipment and expert staff. Many assemblers - programs for genome assembly are available differing in performance, size of the analyzed genome or target organism. The quality of final assembly is fully dependent on assembler and setting of inner parameters. In practice, multiple assemblies are constructed and their quality evaluated according to the technical and biological parameters. The presented thesis describes current high throughput sequencing technologies, different approaches and algorithms for genome assembly and methodology for their quality assessment. The practical part is focused on assembly and its quality assessment using Illumina data of the bird fluke Trichobilharzia szidati.
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Analysis of the genome of a free-living amoeba Mastigamoeba balamuthi and its comparison with pathogenic Entamoeba histolytica
Žárský, Vojtěch ; Tachezy, Jan (advisor) ; Bruchhaus, Iris (referee) ; Beneš, Vladimír (referee)
Charles University, Faculty of Science Department of parasitology Doctoral study programme: Parasitology Abstract (en) Analysis of the genome of a free-living amoeba Mastigamoeba balamuthi and its comparison with pathogenic Entamoeba histolytica Mgr. Vojtěch Žárský Supervisor: prof. RNDr. Jan Tachezy, Ph.D. Praha, 2020 Abstract Examination and comparison of organisms have been tremendously important for the study of life's history on earth. The progress of our understanding of the genetic basis of heredity and the recent boom of sequencing technologies allows us to continue in this exciting field of research from the perspective of genes and genomes. In this work, I focus on the study of an anaerobic amoeba Mastigamoeba balamuthi, which is related to an important human pathogen Entamoeba histolytica. Comparative analysis allows us to draw some conclusions about the nature of the common ancestor of Mastigamoeba and E. histolytica, how it adapted to the anaerobic lifestyle, and about the way the Entamoeba lineage evolved to become a successful parasite. Surprisingly we also noticed that besides hydrogenosomes (hydrogen-producing organelles related to mitochondria), M. balamuthi also harbors peroxisomes - organelles thought to be absent in anaerobic organisms. This finding motivated us to inquire more about...
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Speciation genomics in nightingales
Mořkovský, Libor ; Reifová, Radka (advisor) ; Macholán, Miloš (referee) ; Piálek, Lubomír (referee)
Speciationisusuallyaslowprocessoccurringoverthousandstomillionsofyears.Thismakes speciation research difficult because no direct observation or manipulation is possible. At best, we can gain some insight by inferring the population history and structure in very fine detail by investigating genetic markers in multiple individuals of the nascent species. Today, speciationresearchisinanunprecedentedpositionthankstotheadventofhigh-throughput sequencingmethods,whichmakeiteasier and cheaper than ever before to evaluate multiple markers in many individuals. Speciation is not a straightforward process that happens in the same way every time, but rather a phenomenon occurring when genetic and ecological circumstancesactinginsymphonyultimatelyleadtoreproductiveisolationoftwosubpopula- tions. This is why it is important to study multiple model systems to understand the general principles behind speciation. We worked with two species of nightingales (Luscinia luscinia andL.megarhynchos)thatdivergedapproximately1.8Mya,likelyduetoglacialfluctuations in Europe. Our main goal was to use these new high-throughput sequencing methods to (1) detect interspecific hybrids between the species, (2) estimate levels of interspecific gene flow,(3)findareasofthenightingalegenomethatunderliereproductiveisolationand,finally, (4)...
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Integration site distribution of expressed proviruses
Miklík, Dalibor ; Hejnar, Jiří (advisor) ; Kejnovský, Eduard (referee) ; Indik, Stanislav (referee)
To establish efficient expression of their genes, retroviruses integrate proviral copies into the genomes of the cells they have infected. Epigenetic events, however, silence expression of the integrated proviruses. This silencing protects host cells from harmful viral spread, but also creates a reservoir of latent proviruses that subsequently hinders the cure of retroviral (e.g., HIV-1) infections. Furthermore, the silencing of retrovirus-derived integrative vectors complicates their application in transgenesis and gene therapy. The goal of this thesis is to describe the interaction between retroviral expression and host (epi)genomic environment at the site of proviral integration. To pursue the goal, we sought to define the (epi)genomic environment of the proviruses, which expression is not affected by the epigenetic silencing. Diverse retroviral vectors derived from avian sarcoma and leukosis virus (ASLV), murine leukemia virus (MLV), and human immunodeficiency virus type 1 (HIV-1) were used as model retroviral systems, and expression stability of the vectors in human cell lines was examined. In order to identify the features unique to integration sites of the active proviruses, we sorted the cells positive for the proviral expression, identified their proviral integration sites, and compared them to...
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Evolution of a dog domestication and genetic diversity of the recent breeds.
Ungrová, Lenka ; Černá Bolfíková, Barbora (advisor) ; Vinkler, Michal (referee)
The origin, timing and the developement of the first stages of domestication are the most frequently studied topics within the evolutionary domestication. Even there are a lot of studies, there are also a lot question that have not been answered. Consequent processes are not less interesting. It is known that the first prototypes of dog breeds were formed much earlier before the first breeding clubs were established. We can say, that the first selection was for the type of work which should be carried by the dog, besides the selection for tameness. The next step of selection included selection for the specific phenotypic traits and often involved targeted hybridization between emerging breeds. Over the past 200 years, more than 400 breeds with a unique combination of traits were recognized. This thesis aims to map the emergence of modern breeds from a genetic point of view. Thesis also summarizes the effect of evolution and domestication on specific traits and genes and how they affected the genetic diversity of dog breeds.
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Signs of the Origin and Evolution of Eusociality in Hymenoptera on Genomic Level
Fraňková, Tereza ; Straka, Jakub (advisor) ; Musilová, Zuzana (referee)
Eusociality has evolved independently many times in social Hymenoptera and some of them are now at the brink of eusociality. Eusociality is a complicated set of genomic, ecological and behavioural traits closely interacting with each other. Recent studies presented many interesting outcomes which explain at least partially the possible connections to eusociality on the genomic level. However, the true origin and evolution of eusociality is yet to be refined. Because eusociality is such a dominant quality in the lives of eusocial Hymenoptera, it is important to clarify what causes eusociality to arrise. This thesis summarises the most prominent findings in the field of genomics and reviews not only the outcomes but also the issues of this problematics. The thesis deals with the classification of eusociality, brief introduction to the species lifestyles, which are of great importance for understanding the main part. The main part focuses on the concrete genomic data elucidating possible signs of the evolution of eusociality recognised so far. Key words: eusociality, genomics, evolution, Hymenoptera, Insecta
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Surface phenotype of human carcinoma cancer stem cells (CSC)
Bočková, Marie ; Drbal, Karel (advisor) ; Čermák, Vladimír (referee)
Tumor is composed of a heterogenous mass of cells. Similar to normal healthy organs and tissues, these can be divided into individual cellular subpopulations according to morphology, function and expression patterns. A subpopulation of cells that are able to give rise to all of these cellular lineages is referred to as cancer stem cells (CSC). CSCs have the capabilities of normal stem cells such as the self-renewal and the ability to give rise to a heterogenous population of differentiated cells. Usually, this is the most resistant subpopulation within a tumor, highly non-responsive to therapy. Doing so, they are the cause of residual disease. Characterisation of CSC markers of individual tumor types is beneficial since it enables higher therapy efficacy via targeting this cell population. The -omics approaches to characterisation of the surface proteome bring a broader view into the field when searching for a unique gene signature of specific cancer stem cell types. It has been found that these cells can be identified based on the high expression levels of CD44, CD90 and CD49f. Among other markers, CD47 is an important marker for its immunosuppressive function.
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Implemenation of the RAD sequencing methods to the population genetic studies of hedgehogs from the genus Erinaceus
Loudová, Miroslava ; Černá Bolfíková, Barbora (advisor) ; Choleva, Lukáš (referee)
Hedgehogs from the genus Erinaceus are an important model organism for studying the postglacial recolonisation of Europe and the processes that take place in the secondary contact zones of their areas of distribution. In this study, five individuals of white-breasted hedgehog (Erinaceus roumanicus), four individuals of western hedgehog (Erinaceus europaeus) and one estimated hybrid were analysed. Geographical distribution of individuals used in the study covers the region of the Central Europe, however in the further research expansion of analsysed individuals will be needed and the whole Palearct should be sampled. The main goal was to implement novel methods in research of hedgehogs, which will enable to map the population-genomic structure of the genus Erinaceus in western Palearct. The method RADSeq (Restriction site associated DNA sequencing) enables to obtain polymorphic markers, e.g., SNPs which we used (Single Nucleotide Polymorphisms) across the genome. In this work it was analyzed 16382 SNPs. Using the binary data which indicates the presence and absence of SNPs for each species, hypotheses raised under classical analyzes of genetic markers from previous studies have not been fully confirmed. In further research it will be necessary to verify possible occurrence of biases connected with...
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Genomic approach in speciation studies
Habalová, Kateřina ; Hulva, Pavel (advisor) ; Mikulíček, Peter (referee)
Speciation, adaptation and hybridization are three concepts, each one referring to different process but having a common evolutionary context. Maternal line splits into two sister lines or only one line cleaves from maternal one during speciation. However it leads to formation of new species. Adaptation and hybridization can lead to formation of new species as well. New species arise by adapting to new conditions during adaptation. Within hybridization it is a desecendant of two different lines mating amongst themselves. Most of this thesis is being addressed to these issues, the lesser part is addressed to specific examples. The chapter about next-generation sequencing methods is also included, as these methods have been used more frequently recently. Key words: speciation, adaptation, hybridization, genomics, next-generation sequencing
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