1,720,990 research outputs found
Current genomic and cytogenomic methods in analysis of chromosome rearrangements
Full text linkChromosome 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...Chromozómové přestavby jsou jedním z hlavních mechanizmů evoluce eukaryotických genomů a mohou významně přispět k reprodukční izolaci a diverzifikaci, včetně evoluce komplexních znaků přispívajících např. k lokální adaptaci. Jsou to strukturní změny vedoucí ke změně morfologie a/nebo počtu chromozómů, které mohou mít přímý vliv na evoluci a expresní profily genů, četnost a distribuci rekombinace v genomu a funkční dynamiku procesů v interfázním jádře. Mohou být ovšem také podstatou (nebo doprovodným jevem) vrozených vad a nádorového bujení. Studium chromozómových přestaveb a mechanizmů jejich vzniku souvisí s identifikací a charakterizací oblastí, kde došlo ke dvouvláknovému zlomu a opětovnému spojení částí chromozómů. Jednou z možností je analyzovat chromozómy a mezidruhové změny v uspořádání vazebných skupin/syntenních bloků pomocí cytogenetických a cytogenomických metod (např. mezidruhovým mapováním celochromozómových hybridizačních sond). Detailnější vhled přináší srovnávací genomika, v dnešní době zastoupená především tzv. metodami třetí generace (platformy firem PacBio a Oxford Nanopore Sequencing), často v kombinaci s dalšími pokročilými metodami jako jsou Hi-C nebo optické mapování. Cílem této bakalářké práce je shrnout současné přístupy v analýze chromozómových přestaveb (včetně...Katedra genetiky a mikrobiologieDepartment of Genetics and MicrobiologyPřírodovědecká fakultaFaculty of Scienc
The comparison of animal species determination (barcoding) methods
Full text linkDruhová identifikace je klíčovým prvkem v mnoha vědních oborech, od studia diverzity až po forenzní vědy a potravinářský průmysl. Tradiční morfologické metody založené na vizuálním rozlišení anatomických rysů často narážejí na limity spojené s určováním morfologicky podobných živočichů. S nástupem molekulárních metod se však objevila nová perspektiva, a to analýza DNA, která nabízí vyšší přesnost a nezávislost na vnějších faktorech. V této bakalářské práci je popsán podrobný přehled a srovnání různých molekulárních metod, které slouží k identifikaci živočichů. Zaměřuje se na důkladné zhodnocení principů fungování těchto metod a jejich efektivity. Zvláštní pozornost je věnována cílovým sekvencím spojeným s DNA barcodingem, jeho univerzálnímu využití a omezením, která mohou vzniknout v závislosti na konkrétním druhu živočichů. Důležitým prvkem úspěšné identifikace je existence a využívání databází, které slouží jako zdroj referenčních dat pro porovnání sekvencí z neznámých vzorků.Species identification is the key element in many scientific fields, from diversity studies to forensic science and the food industry. Traditional morphological methods based on the visual distinction of anatomical features often encounter limits associated with distinguishing morphologically similar animals. However, with the rise of molecular methods, a new perspective has emerged, namely DNA analysis, which offers higher accuracy and independence from external factors. This bachelor's thesis presents a detailed overview and a comparsion of various molecular methods used to identify animals. It focuses on a thorough evaluation of the principles of these methods and their effectiveness. Special attention is paid to target sequences associated with DNA barcoding, its universal use and limitations that may arise depending on specific animal species. An important element of successful identification is the existence and use of databases that serve as a source of reference data to compare sequences from unknown samples.Department of Genetics and MicrobiologyKatedra genetiky a mikrobiologiePřírodovědecká fakultaFaculty of Scienc
Karyotype analysis of mygalomorph spiders of the families Hexathelidae and Dipluridae
No full textCytogenetics of spiders of the infraorder Mygalomorphae is largely unknown. My thesis is focused on the karyotype evolution of spiders of families Hexathelidae Dipluridae, which are basal groups of the superfamily Avicularioidea. In this thesis the evolution of diploid chromosome number, chromosome morfology, and also sex chromosomes are studied. The karyotypes of the mygalomorphs are quite interesting for their diversity. Many members of the family Hexathelidae exhibit extreme systems of a chromosomal sex determination which are composed by many gonosomes X. The meiotic division of males is analyzed. Some species exhibit modifications of this division such as achiazmatic meiosis. Selected markers have been detected by fluorescence in situ hybridization. Keywords: evolution, fluorescent in situ hybridization, karyotype, nucleolus organizer region, sex chromosomes, spide
Karyotype evolution of the family Araneidae
No full textOrb-weavers (Araneidae) are a diversified spider family comprising more than 3,100 species in more than 170 genera. Together with 13 other families, they con- stitute to superfamily Araneoidea. The presented thesis focuses on karyotype evo- lution of Araneidae, including its comparison with a related family Tetragnathidae. The results obtained from 19 araneid and four tetragnathid species confirm previ- ously postulated hypothesis that the ancestral karyotype of Araneoidea (including Araneidae) consists of 24 acrocentric chromosomes in males, including two acro- centric X chromosomes of system X1X20. However, there is a tendency of 2n decrease in some araneids due to centric fusions. In these cases, centric fusions affected most autosomes (and sometimes gonosomes as well); number of chromosome pairs de- creased from 11 to six. Three independent reduction events were detected in this thesis. Furthermore, pattern of nucleolar organizer regions (NORs) was studied in this thesis using fluorescent in situ hybridization, since data on evolution of this marker are scarce in spiders. Striking variability in NORs number was discovered, ranging from one to 13 loci. Remarkably, multiple centric fusions were always ac- companied by considerable increase of NORs number. In araneids and tetragnathids possessing..
Current genomic and cytogenomic methods in analysis of chromosome rearrangements
No full textChromosome 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..
The comparison of animal species determination (barcoding) methods
No full textSpecies identification is the key element in many scientific fields, from diversity studies to forensic science and the food industry. Traditional morphological methods based on the visual distinction of anatomical features often encounter limits associated with distinguishing morphologically similar animals. However, with the rise of molecular methods, a new perspective has emerged, namely DNA analysis, which offers higher accuracy and independence from external factors. This bachelor's thesis presents a detailed overview and a comparsion of various molecular methods used to identify animals. It focuses on a thorough evaluation of the principles of these methods and their effectiveness. Special attention is paid to target sequences associated with DNA barcoding, its universal use and limitations that may arise depending on specific animal species. An important element of successful identification is the existence and use of databases that serve as a source of reference data to compare sequences from unknown samples
Sex chromosome evolution in ray-finned fishes (Actinopterygii)
Full text linkRay-finned fishes (Actinopterygii) possess strikingly diverse sex sex differentiation strategies (including gonochorism, unisexuality and several types of hermaphroditism) and mechanisms of sex determination (both environmental and genetic), including frequent turnovers between abovementioned strategies and mechanisms. Although exhibiting remarkable diversity of sex determination mechanisms, only about 5% of analyzed teleost species possess cytologically recognizable (i.e. heteromorphic) sex chromosomes. Still, nine different male- or female- heterogametic sex chromosome systems at various stages of differentiation have been described along with high rate of inter- and intraspecific variability. Given that early sex chromosome evolution is best studied in evolutionarily young nascent sex chromosomes, ray- finned fishes and especially the teleost lineage (Teleostei) represent vital model group for these investigations offering new insights into the evolution of these rapidly evolving regions of vertebrate genomes. Moreover, handful of studies available so far has provided evidence for a role of emerging sex chromosomes and their turnover in processes such as ecologial adaptation, speciation or genomic conflict. Besides cytogenetic studies, which had a major impact on our current knowledge about fish..
Robertsonian translocations and their involvement into genome evolution
Full text linkChromosome aberrations play an important role in human pathologenesis as well as in evolution of many organisms. Robertsonian translocation or centric fusion are the most frequent chromosomal rearrangements in mammals. The most investigated model for their research is house mouse Mus musculus. The standard karyotype of a mouse consists from 40 acrocentric chromosomes, notably there are more than one hundred wild populations that are characterized by various combination of metacentrics, formed by centric fusion of different acrocentrics. Several models have been proposed for the formation of metacentrics, taking account of the sequential structure of their centromeres and short arms in mouse. Segregation distortion in favor of metacentrics is present in female and/or male meiosis, such as meiotic drive can positively affect the degree of fixation of metacentric chromosomes in certain population. Centric fusions have been also presented in evolution of other organisms. Cytogenetic data in spiders indicate the possibility of similar phenomena in the most diversified group of spiders, Entelegynae. Spiders are notable for their unusual sex chromosome systems. Centric fusions also play an important role in the evolution of sex chromosomes and the formation of neo-sex chromosome systems. So far, there is..
Analysis of karyotype and sex chromosome differentiation in African annual killifish of the genus Nothobranchius (Teleostei: Nothobranchiidae)
Full text linkTeleost fishes (Teleostei) encompass more than half of the extant vertebrate biodiversity. Their genomes display considerable plasticity and flexibility, going hand in hand with polyploidization events and repetitive DNA dynamics. Teleosts also display a striking diversity in mechanisms of sex determination and differentiation. The aim of the present thesis was to study the mechanisms underlying the karyotype and sex chromosome differentiation through cytogenetic mapping of repetitive DNA (by fluorescence in situ hybridization, FISH) in selected representatives of the African annual killifishes of the genus Nothobranchius (Teleostei: Nothobranchiidae). Nothobranchius spp. evolved a unique adaptation to freshwater temporary water pools whose existence is limited to periods of rainy season in African savannahs. Recent diversification, allopatric speciation in non-overlapping generations and small-sized populations together with known cytogenetics collectively suggest fast dynamics of chromosomal changes in Nothobranchius killifishes. The study took advantage of the availability of i) more populations of several closely related species for analysis and ii) data on specific repetitive DNA composition in selected Nothobranchius genomes as revealed by RepeatExplorer analysis. My work showed considerable..
Evolutionary pattern and mechanism of environmental sex determination in reptiles.
No full textEven though environmental sex determination (ESD) was described almost 60 years ago, our understanding of its mechanisms and evolution remains fragmentary. In ESD, there is no consistent genetic difference between males and females; instead, the sex of an individual depends on environmental stimuli. This contrasts with genotypic sex determination (GSD), where specific genetic factors determine sex. Recent advances in molecular tools have significantly impacted sex determination research. First, the identification of sex chromosomes has revealed GSD in many amniote lineages, leading to the reclassification of many species previously thought to exhibit ESD. This indicates that the prevalence of ESD among reptiles was previously overestimated. Second, molecular tools have enabled transcriptomic studies of ESD during the key phases of their embryonic development. They identified potential players, including epigenetic modifiers (like demethylase kdm6b) and calcium signalling, particularly in the turtle model species Trachemys scripta. These findings led to the proposal of an overarching model that combines calcium signalling and oxidative stress, highlighting the role of temperature-sensitive ion channels. Additionally, other mechanisms, such as stress and related hormones and the impact of germ cell..
- …
