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Phylogenomics, genome size evolution and repeat dynamics in the genus Amomum Roxb. (Zingiberaceae)
Hlavatá, Kristýna ; Fér, Tomáš (advisor) ; Haevermans, Thomas (referee) ; Zedek, František (referee)
Amomum Roxb. s.l. (black cardamom) is a complicated genus in the ginger family Zingiberaceae (subfamily Alpinioideae) that according to some definitions includes groups of species recognized as separate genera, e.g. genus Elettariopsis Baker. Phylogenetic studies have so far failed to elucidate both the position of Amomum within Alpinioideae and the relationship between Amomum and other genera like Elettariopsis. In this work, Amomum was subjected to a detailed morphological analysis of the largest possible sampling, together with a phylogenetic analysis. Amomum was recircumscribed, Amomum s.s. and three new genera were established, three genera were resurrected, and genus Elettariopsis was merged into Amomum. Meanwhile, new species were described and others epitypified. A well-resolved nuclear-gene phylogeny of Amomum s.s. was obtained using next-generation sequencing (Hyb-Seq) and showed the existence of four clades (A, B, C, D) within the genus. Clade D, the former genus Elettariopsis, was further divided into three subclades (D1-D3). A chloroplast DNA-based phylogeny supported this structure, but additional phylogenies based on ribosomal DNA were incongruent with it, indicating that the frequently used ITS marker and other rDNA markers may not be suitable for reconstructing deeper phylogenetic...
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Evolution of members of the genus Cardamine from the Anatolia-Caucasus region and the Balkan Peninsula
Kantor, Adam ; Slovák, Marek (advisor) ; Frajman, Božo (referee) ; Tribsch, Andreas (referee) ; Oberprieler, Christoph (referee)
This thesis aims to elucidate evolution of the members of the selected species groups of the genus Cardamine, which is a species-rich genus with cosmopolitan distribution and very complex evolutionary history. The studied species were represented by hygrophytic perennials, with the focus laid on their diversity in the Balkan Peninsula and Southwestern Asia, with the emphasis put on the Anatolica-Caucasus region. These regions harbour global biodiversity hotspots and important glacial refugia, yet, they have been largely understudied in terms of knowledge of evolutionary mechanisms and environmental factors that have played there a role of plants diversification and speciation drivers. In this thesis, questions concerning the phylogeny and taxonomy of the studied groups were addressed, with aim to determine the role of polyploidy and hybridization in their evolution. Hyb-Seq was the majorly applied method, representing a technique based on next-generation sequencing, which has proven to be a very efficient and versatile method for resolving evolutionary questions. An integrative approach was employed, combining Hyb-Seq with a variety of other karyological, molecular, cytogenetic and ecological niche modelling methods, which provided a very complex insight into the addressed topics. This thesis...
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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.
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Application of Hyb-Seq method for reconstruction of reticulate infrageneric phylogeny: example from polyploid genus Curcuma L. (Zingiberaceae)
Skopalíková, Jana ; Fér, Tomáš (advisor) ; Krak, Karol (referee)
This master thesis focuses on the phylogeny of hybridogenous and polyploid genus Curcuma from family Zingiberaceae using Next-Generation Sequencing data from hundreds to thousands nuclear loci. This approach seems to be better than widely used cpDNA and ITS sequencing especially in the case of hybridogenous and polyploid groups. Data for phylogeny reconstruction were generated using Hybridization-based sequencing (Hyb-Seq) method which combines target enrichment and genome skimming strategies. Data analysis was performed primarily using pipeline HybPhyloMaker especially created for Hyb-Seq data analysis. Twenty-seven species from the genus Curcuma and three outgroup species were sequenced in this work. Phylogenetic trees based on all 1 154 and 811 selected nuclear low- copy genes show high support values of all nodes which is in contrast to plastome and rDNA phylogeny with lower support values in some nodes and incongruences in topology compared to low-copy genes phylogeny. Phylogenetic networks inferred from low-copy genes, lineage movement analysis and monophyly tests agree with published hypotheses of interlineage hybrid origin of three species - C. vamana, C. myanmarensis and C. roscoeana. These analyzes show likely hybrid origin of C. candida too with parents from the group Curcuma I and basal...
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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.
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