|
|
Application of next-generation sequencing for phylogenetic reconstruction of polyploid plants
Skopalíková, Jana ; Fér, Tomáš (advisor) ; Šrámková, Gabriela (referee)
This bachelor thesis summarizes available information about currently used next- generation sequencing (NGS) methods where a big progress was achieved during last few years. Great advantage of NGS is the ability to gain huge amount of data at much lower cost per base compared to the Sanger sequencing. However, there are various pitfalls in data analysis. Nowadays it is possible to sequence the entire genomes of individuals. Nevertheless, this approach remains challenging when studying many individuals, e.g. in phylogenetics. Recently, several approaches for effective reduction of genome complexity arose: transcriptome sequencing (RNA-Seq), target enrichment, restriction digest-based methods (RAD-Seq, RLL, GBS), genome skimming (shallow sequencing), etc. Each method has both advantages and disadvantages that affect its utility in phylogenetics. Furthermore, the thesis deals with polyploid speciation and particularity of phylogenetics in polyploid plants - selection of suitable markers followed by data processing and phylogenetic analyzes. The last part of the thesis is devoted to my future research of polyploid genus Curcuma L.
|
|
|
Sources of Sorbus aria agg. variation
Bílá, Jana ; Urfus, Tomáš (advisor) ; Krahulec, František (referee)
The main drivers of microevolution in the genus Sorbus are interspecific hybridisation and polyploidy. The fate of new hybrid and polyploid taxa is determined by their mode of reproduction. Especially apomixis could be very advantageous for these new taxa. The S. aria agg. (subg. Aria) plays an important role within the genus since its members are involved in all hybridisation events and thereby is responsible for the substantial part of variation of the genus. Flow cytometry, molecular markers and multivariate morphological analyses were employed to evaluate the processes generating the variability in the S. aria group. Three ploidy levels were detected among species from subg. Aria in the Czech Republic. All of them could be found in the South Moravia, whereas only tetraploids occur in the Bohemia region. Moreover, most of the Czech taxa (5 out of 7) grow also only in the South Moravia which is therefore considered as a centre of diversity of the genus Sorbus in the Czech Republic. Flow cytometry seed screen revealed 7 modes of reproduction among the individuals from S. aria agg. A wide range of sexual and apomictic types of reproduction including reduced and unreduced gametes was detected. All of the diploid individuals are completely sexual. Among polyploid taxa, most of the species are...
|
|
|
Evaluation of cytotype and morphological variability and hybridization rate in water-milfoils (Myriophyllum) in the Czech Republic and adjacent territories
Hrdinová, Magdalena ; Trávníček, Pavel (advisor) ; Koutecký, Petr (referee)
Myriophyllum L. (watermilfoil) belongs to one of the most invasive genus of the Northern Hemisphere. The three most agressive species, one of which is native to Europe (M. spicatum), are widespread throughout the majority of United states and two of them (M. aquaticum and M. heterophyllum) are becoming invasive in several Europaean countries as well. Therefore, Europaean populations of both native and invasive species, represents ideal place where to study processes which account for watermilfoils' invasivness. In this study, flow cytometry, morphometric analyses and germination experiments were employed to evaluate cytotype and morphological variability of Myriophyllum along with its potential to hybridize and propagate generatively. Five ploidy levels were detected in Europe, however no ploidy variability has been found within any species except for M. sibiricum (hexaploids and nonaploids) and one population of M. aquaticum (hexaploids and oktoploids). Flow cytometry proved to be useful tool for purposes of distinguishing species of different ploidy level and their potential hybrids. Nevertheless, the key species - M. sibiricum and M. spicatum - among which probably even more aggressive hybrids were recently identified, have similar hexaploid level. Thus flow cytometry cannot facilitate...
|
|
|
Effect of polyploidization on species invasive success
Líblová, Zuzana ; Münzbergová, Zuzana (advisor) ; Rooks, Frederick (referee)
Polyploid variants of many species of plants are strikingly frequently found among alien plants on all continents. They also very often have a much larger distribution range of its occurrence, compared to diploid plants in the place of their origin. In many cases, the polyploid cytotype also has increased tolerance to various stress factors or a physiological and morphological characteristics that allow them to survive the conditions in which the diploid plants would have little chance to survive. All this suggests that polyploidy is likely to bring plants an evolutionary advantage over their diploid ancestors, and polyploids therefore can successfully colonize new territories. This thesis summarizes the findings about the possible consequences of polyploidy at different levels in relation to their effects on the properties supporting plant invasive ability. It presents also known hypotheses dealing with possibilities of why plants become invasive after introduction. This is followed by sections devoted to flow cytometry, an important modern method for determining genome size and ploidy level. In conclusion it briefly describes the model species bird vetch (Vicia cracca) and the results of measurements of the degree of ploidy of seeds of this plant from Alaska and Japan.
|
|
|
Polyploidy with specific view to paleopolyploidy and its detection
Kotz, Matěj ; Král, Jiří (advisor) ; Rothová, Olga (referee)
Polyploidy is a significant phenomenon in the evolution of eucaryotic organisms. It has been a subject of interest of biologists for decades and it has been studied particularly largely in plants, where it most often occurs. This thesis handles occurrence of poylploidy in organims and a special emphasis is laid on old polyploidization events occurrence of polyploidy in animal taxa. Furthermore, the types of polyploidy and obstacles are discussed here, that a polyploid organism has to tackle to stabilize its genome. That also includes the need to ensure the correct chromosome segregation in a meiotic division. A special case of polyploidy is paleopolyploidy (sometimes refered to as "ancient polyploidy" in English), which is an evolutionary old polyploidization event, that is followed by the process of diploidization. This process is characterized besides others by a large number of structural changes in chromosomes and a loss of some DNA sequences and a gradual transition of the polyploid genome to the cytologically diploid state. Because of these changes, it is difficult to detect a paleopolyploidy and the main part of this thesis is dedicated to this problem, in which the main approaches that might lead to its detection are discussed. Key words: polyploidy, animal, plant, meiosis, paleopolyploidy,...
|
|
|
Ecological and evolutionary processes in primary contact zone of cytotypes of Knautia arvensis agg.
Hanzl, Martin ; Kolář, Filip (advisor) ; Urfus, Tomáš (referee)
Genome duplication events have played a crucial role in plant evolution. According to recent estimates, nearly all the angiosperms are ancient polyploids. However, establishment of new polyploid lineages within diploid populations seemed to be very unlikely, based on theoretical analyses. Reproductive interactions between the cytotypes (so-called "minority cytotype exclusion") and resource competition might eventually lead to polyploid extinction. On the other hand, the whole variety of factors may compensate both processes under natural conditions (e.g. autogamy, assorative mating, spatial separation of cytotypes). Polyploid establishment in sympatry with diploid progenitor might thus not be as restricted, as previously thought. Subsequent cytotype coexistence may represent a stable equilibrium, or just a transition leading to extinction of one chromosomal race. It is usually almost impossible to discriminate between these alternatives. Polyploid range expansions are usually accompanied by competitive exclusion of diploid cytotype or colonization of new areas and habitats. When two cytological races meet, zones of contact are often formed. Contact zones could be divided into primary and secondary ones. Primary contact zones arise as a consequence of new polyploid emergence within the progenitor's...
|
|
|
Sources of Sorbus aria agg. variation
Bílá, Jana ; Urfus, Tomáš (advisor) ; Chumová, Zuzana (referee)
Genus Sorbus is a very complex group of vascular plants. Various genetic lineages which can be fixed by apomixis are driven by interspecific hybridisation and polyploidy. Species from S. aria agg. have the highest variation probably due to an extra mechanism - introgressive hybridisation. There are several concepts of the aggregate which are usually based on three main species: S. aria, S. umbellatta and S. graeca. Therefore, new microspecies are derived by genome doubling and hybridisation between the main species. Units of the aggregate are assessed differently as the distinction of taxa is very complicated due to the overlap of the morphological variability. The aggregate itself can be sometimes considered as a category for species of uncertain origin or identification. Four species from S. aria agg. occur in the Czech Republic. In addition, the conclusion offers questions that will be addressed in the master's thesis.
|
|
|
Risk assessment of interspecific hybridization between endemic Campanula bohemica and widespread C. rotundifolia s.l.
Hanušová, Kateřina ; Suda, Jan (advisor) ; Krahulec, František (referee)
The thesis deals with phenotypic, ploidy and genetic variation of two Campanula species occurring in the Krkonoše Mts., namely the endemic C. bohemica and widespread C. rotundifolia subsp. rotundifolia. For comparative purposes subspecies sudetica of the latter species was also included. The main aim was to get insight into population structure and assess the threat of interspecific hybridization to the survival of the endemic bluebell. Flow cytometry, distance-based morphometrics and molecular analysis were used to address these questions. Three distinct groups of fluorescence intensities were revealed by flow cytometry, corresponding to DNA diploids, tetraploids and pentaploids. While diploids morphologically matched the nominate subspecies of C. rotundifolia, tetraploids corresponded either to C. rotundifolia subsp. sudetica or C. bohemica. Most populations from the Krkonoše Mts. were uniform although a sympatric growth of diploids and tetraploids was encountered in 12 populations. Only two pentaploids individuals, most likely of hybrid origin, were found, which indicated that interspecific hybridization is much less common than previously assumed. The two tetraploid taxa were distinguished by molecular markers. A combination of flow cytometry and molecular analyses thus allowed reliable...
|
|
|
Watermilfoils (Myriophyllum) in the central Europe
Hrdinová, Magdalena ; Trávníček, Pavel (advisor) ; Prančl, Jan (referee)
Genus Myriophyllum L. (watermilfoil) belongs to one of the most species-rich genera within Haloragaceae (Saxifragales). It includes three invasive species, which are of major concern - European M. spicatum L., North American M. heterophyllum MICHX. and South American M. aquaticum (VELL.) VERDC. All of them occur in Central Europe as well as native M. verticillatum L. and M. alterniflorum DC. lacking more significant invasive growth up to now. It is not only its invasivness that makes genus Myriophyllum so fascinating. It also displays extremely high phenotypic plasticity which is accompanied by determination difficulties. Moreover, recent research indicates that Myriophyllum tends to hybridize producing more invasive hybrids than parental taxa. Such traits pose a formidable challenge to scientists to deal with possible future invasive growth of non-indigenous Myriophyllum species in Central Europe. Therefore, thorough study of factors influencing evolution success of plants should be conducted. One of the key factors seems to be polyploidy. Research into polyploidy offers a new approach to watermilfoil issues. Additionally, according to preparatory study all native Central European Myriophyllum species can be easily distinguished by flow cytometry. That enables to study polyploidy in an...
|
|
|
Conservation aspects of endemism in Central Europe with special respect to genus Sorbus
Tesařová, Anna ; Urfus, Tomáš (advisor) ; Macková, Lenka (referee)
Endemit is an organism living exclusively within a particular area on Earth. There are several mutually interconnected mechanisms leading to endemism i.e. allopathic speciation, polyploidization, hybridization and apomixis. This thesis deals with describing particular modes of endemic speciation and their occurrence. The most significant concept is certainly discrimination of paleoendemites and neoendemites. Paleoendemites are very rare and within Central Europe occur scarcerly only in Western Carpathians. Neoendemites are hardly comparable among Central European states. The concentration of endemics is closely related to the global centers of diversity that are distributed in highly unbalanced way. The genus Sorbus is essential group with regard to endemism in Central Europe. That is why the experimental part of my thesis was focused on flowcytometric analyses (absolute genome size and DNA ploidy level) of 13 endemic Sorbus species. Triploidy was proved to be prevailing ploidy level. Among triploid samples 6% of variation was recorded. The absolute genome size of the remaining endemic taxa indicated tetraploid level.
|
guest ::
