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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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Evaluation of variability within Sparganium erectum using morphometrics, AFLP and flow cytometry
Píšová, Soňa ; Fér, Tomáš (advisor) ; Kaplan, Zdeněk (referee)
MSc. thesis is based on evaluation of intraspecific morphological and genetic variation of Sparganium erectum L. in the Czech Republic. Four intraspecific taxa were examined: S. erectum subsp. erectum L., S. erectum subsp. oocarpum (ČELAK.) DOMIN, S. erectum subsp. neglectum (BEEDY) RICHTER and S. erectum subsp. microcarpum (L.M. NEUMANN) DOMIN. Various approaches such as multivariate morphometric analysis (PCA, discriminant analyses), estimation of genome size by propidium iodide flow cytometry and molecular analysis of total genomic DNA (AFLP) were applied for study close related subspecies. Multivariate analysis of morphological characters of fruits (for 350 individuals from 63 native populations) presented some distribution to four closed groups. Partial overlapping was observed for S.erectum subsp. neglectum with subsp. microcarpum and subsp. oocarpum. Similar situation (overlapping subsp. neglectum a microcarpum) was observed within genome size. Remaining two taxa, S. erectum subsp. erectum and subsp. oocarpum, were well-differentiated using genome size data. Most important morphological characters on fruits useful for subspecies determination were: sterility of fruit heads, presence or absence of peduncle, distinct shoulder between upper and lower part, constriction below the shoulder, width of fruit...
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Genome size evolution in the Zingiberaceae
Pospíšilová, Monika ; Fér, Tomáš (advisor) ; Kolář, Filip (referee)
The purpose of this study is to evaluate the existing knowledge on the evolution of genome size and also to focus on genome in the phylogenetic context. Among angiosperms we find a wide range of C-values (1C = 0.63 pg ? 1C = 127.4 pg), but the modal value is 0.6 pg. We still do not know much about the nature and mechanisms of plant genome size evolution, but we are learning more and more every year. There are already dozens of studies dealing with the dynamics of genome size of smaller taxonomic groups and on four of these they demonstrate possible approaches. Researching within higher taxonomic groups such as families is difficult and so more valuable. New research on the evolution of genome size in the family Zingiberaceae has started and my master thesis dealing with the Globbeae tribe should be part of it.
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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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Genome size evolution in tropical tribe Globba (Zingiberaceae)
Pospíšilová, Monika ; Fér, Tomáš (advisor) ; Zedek, František (referee)
The variability of the genome size reaches several grades even within relatively close groups of plants. The study of the genome size in the phylogenetic context provides interesting results which characterize the evolution of the individual groups of plants. In this respect, tropical plants have yet not been studied. Tropical genus Globba (ca. 100 species) belongs to an economically significant family Zingiberaceae. The diversity centre is found in Thailand but it spreads from east India and southern China up to Indonesia and the Philippines. It is a polyploid complex which exists in two cytotypes within one genus (2n = 32 a 2n = 48); it is characteristic minimally in three out of seven distinguished sections. The aim of this thesis has been a reconstruction of the group phylogeny, discovering the role of the polyploid and evaluation of the genome size evolution of the Globba genus in the phylogenetic context. To this end, modern biosystematic methods were used (flow cytometry, chromosome counting, sequencing of the nuclear and chloroplast DNA regions). Many types of software and statistical methods were used to process and interpret the data. In this group, the genome size was measured for the first time. Out of 87 individuals, the smallest size was measured with Globba nuda (2C = 1.11 pg). The...
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Homoploid hybrid speciation in closely related taxa of wetland plants
Píšová, Soňa ; Fér, Tomáš (advisor) ; Albach, Dirk Carl (referee) ; Koutecký, Petr (referee)
6 Summary Wetland plants share several common characters, such as clonality, wind pollination and self-compatibility that facilitate hybridization, especially in complexes of closely related taxa. In this thesis, a Sparganium erectum complex of four subspecies and 14 species of the genus Bolboschoenus were investigated to detect hybridization and verify the origins of putative hybrids. The first part of the thesis is dedicated to an introduction to hybridization, a process of great evolutionary impact, and its several general consequences, which are broadly discussed with numerous examples. In addition, an introduction to the studied taxa is provided as well as the main results of three papers that are presented and discussed herein. The second part of the thesis consists of three papers on hybridization within the Sparganium erectum aggregate (Paper I) and in the genus Bolboschoenus (Paper II, central European species; Paper III all 14 species worldwide). AFLP molecular marker analysis, sequencing of nuclear and chloroplast DNA, and genome size and morphometric analyses were applied to elucidate the genetic relationships among taxa and to confirm the suitability of morphometric characters for taxa and hybrid delimitation. The results clearly present the differentiation of individual taxa and their stable...
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