Frantisek ZedekMasaryk University | MUNI · Department of Botany and Zoology
Frantisek Zedek
Ph.D.
Evolution of genome size - a new role for the centromere drive
About
73
Publications
13,827
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547
Citations
Citations since 2017
Introduction
Additional affiliations
February 2017 - present
January 2017 - December 2019
Position
- Success of holocentric chromosomes: natural competitive experiment on a global evolutionary scale (GA17-21053S)
January 2017 - December 2019
Position
- Success of holocentric chromosomes: natural competitive experiment on a global evolutionary scale (GA17-21053S)
Education
April 2008
Masaryk University, Faculty of Pharmacy
Field of study
- real-time PCR course (Applied Biosystems)
February 2008
Independent Researcher
Field of study
- real-time PCR workshop (Tataa Biocenter)
September 2006 - August 2013
Publications
Publications (73)
Genome size and GC content are basic species-specific attributes often delimiting genera or higher taxa, which enable the identification of polyploidy, hybridization, and other modes of genome or karyotype evolution. The evolution of these genomic traits can often occur under selective pressure of the environment. Here, we reconstruct the evolution...
(1) Evolution of genome size is shaped by various intrinsic and extrinsic factors. We explored three long-standing hypotheses concerning factors shaping the global distribution of genome size: the mutational hazard hypothesis, the polyploidy-mediated hypothesis and the
climate-mediated hypothesis.
(2) We compiled the largest genome size dataset to...
Using molecular data and representative species coverage, we confirmed the monophyly of Cirsium sect. Eriolepis and, therefore, we propose to treat it as a separate genus (Lophiolepis). Besides, based on molecular and morphological evidence we segregate Cirsium italicum into the separate genus Epitrachys, sister to a large clade including Carduus,...
• Background and Aims: While variation in genome size and chromosome numbers and their consequences are often investigated in plants, the biological relevance of variation in chromosome size remains poorly known. Here, we examine genome and mean chromosome size in the cyperid clade (families Cyperaceae, Juncaceae, Thurniaceae), which is the largest...
Background and Aims: In eukaryotes, the total kinetochore size (defined as a chromosomal region containing CENH3-positive nucleosomes) per nucleus strongly correlates with genome size, a relationship that has been hypothesized to stem from general intracellular scaling principles. However, it could also come from the mechanics of the cell division,...
Plants continuously face stress from ultraviolet-B radiation that can cause chromosomes to fragment. The impact of fragmentation may depend on chromosome type: holocentric chromosomes tolerate fragmentation but monocentric chromosomes do not. Our field experiments on holocentric cyperids and monocentric grasses suggested that holocentric plants mig...
Previous studies on grass species suggested that the total centromere size (sum of all centromere sizes in a cell) may be determined by the genome size, possibly because stable scaling is important for proper cell division. However, it is unclear whether this relationship is universal. Here we analyze the total centromere size using the CenH3-immun...
Previous studies on grass species suggested that the total centromere size (sum of all centromere sizes in a cell) may be determined by the genome size, possibly because stable scaling is important for proper cell division. Here we analyze the total centromere size using the CenH3-immunofluorescence area as a proxy in 130 taxa including plants, ani...
Centromere drive model describes an evolutionary process initiated by centromeric repeats expansion, which leads to the recruitment of excess kinetochore proteins and consequent preferential segregation of an expanded centromere to the egg during female asymmetric meiosis. In response to these selfish centromeres, the histone protein CenH3, which r...
Previous studies suggested that holocentric chromosomes may confer a selective advantage under high ionizing or UV-B radiation due to their tolerance of fragmentation, and that the first plant and animal colonizers of land in the Palaeozoic were or may have been holocentric. Holocentric chromosomes could have, therefore, aided terrestrialization of...
Background and Aims: UV-B radiation damages the DNA, cells, and photosynthetic apparatus of plants. Plants commonly prevent this damage by synthetizing UV-B protective compounds. Recent laboratory experiments in Arabidopsis and cucumber indicate that plants can also respond to UV-B stress with endopolyploidy. Here we test the generality of this res...
Premise: It has been repeatedly shown that the remarkable variation of the genome
size of angiosperms can be shaped by extrinsic selective pressures, including nutrient
availability. Carnivory has evolved independently in ten angiosperm clades, but all
carnivorous plants share a common affinity to nutrient-poor habitats. As such, carnivory
and geno...
It has been hypothesized that species with holocentric chromosomes have a selective evolutionary advantage for developmental and reproductive success because holocentric chromosomes are less susceptible to chromosome breakage than monocentric chromosomes. We analyzed data on sterilizing doses of ionizing radiation for more than 250 species of arthr...
Holocentric chromosomes have evolved in various plant and animal taxa, which
suggests they may confer a selective advantage in certain conditions, yet their
adaptive potential has scarcely been studied. One of the reasons may reside in our
insufficient knowledge of the phylogenetic distribution of holocentric chromosomes
across eukaryotic phylogeny...
Online Resource 1. Examples of flow histograms with the calculations of the G2/G1 ratios.
Online Resource 2. G2/G1 ratios of all analyzed samples.
Background: The dispersed occurrence of holocentric chromosomes across eukaryotes implies they are adaptive, but the conditions under which they confer an advantage over monocentric chromosomes remain unclear. Due to their extended kinetochore and the attachment of spindle microtubules along their entire length, holocentric chromosomes tolerate fra...
This corrects the article DOI: 10.1038/srep27161.
Background and Aims: Studies in the carnivorous family Lentibulariaceae in the last years resulted in the discovery of the smallest plant genomes and an unusual pattern of genomic GC content evolution. However, scarcity of genomic data in other carnivorous clades still prevents a generalization of the observed patterns. Here the aim was to fill thi...
• Background and Aims: The centromere drive theory explains diversity of eukaryotic centromeres as a consequence of the recurrent conflict between centromeric repeats and centromeric histone H3 (CenH3), in which selfish centromeres exploit meiotic asymmetry and CenH3 evolves adaptively to counterbalance deleterious consequences of driving centromer...
The centromere drive model explaining rapid evolution of eukaryotic centromeres predicts higher
frequency of positive selection acting on centromeric histone H3 (CenH3) in clades with asymmetric
meiosis compared to the clades with only symmetric meiosis. However, despite the impression one
might get from the literature, this key prediction of the c...
Two chromosomal structures, known as monocentric and holocentric chromosomes, have evolved in eukaryotes. Acentric fragments of monocentric chromosomes are unequally distributed to daughter cells and/or lost, while holocentric fragments are inherited normally. In monocentric species, unequal distribution should generate chimeras of cells with diffe...
[This corrects the article DOI: 10.1371/journal.pone.0030496.].
The alignment of CENH3HCP-3 both prior and after the removal of unreliable regions.
(DOC)
Similar to how the model of centromere drive explains the size and complexity of centromeres in monocentrics (organisms with localized centromeres), our model of holokinetic drive is consistent with the divergent evolution of chromosomal size and number in holocentrics (organisms with non-localized centromeres) exhibiting holokinetic meiosis (holok...
Polyploidy and increased genome size are hypothesized to increase organismal nutrient demands, namely of phosphorus (P), which is an essential and abundant component of nucleic acids. Therefore, polyploids and plants with larger genomes are expected to be selectively disadvantaged in P-limited environments. However, this hypothesis has yet to be ex...
Using flow cytometry, we analyzed genome size (2C, nuclear DNA amount) and genomic base composition (GC content) in more than 600 taxa of Cyperaceae + Juncaceae + Thurniaceae covering representatively all main lineages of this Cyperid clade. Compared to representatives of the other 13 families in Poales, the evolution of the holokinetic chromosome...
In contrast to the “normal type” of monocentric mitotic chromosomes, where spindle attachment is restricted to a single kinetochore, holocentric chromosomes are those in which spindle microtubules attach along the whole length through kinetochores that cover a substantial part of thein poleward surfaces during mitosis. In addition, holocentric sist...
The alignment of CENP-CHCP-4 both prior and after the removal of unreliable regions.
(DOC)
The WormBase gene IDs and GenBank accession numbers and the list of corresponding species.
(XLS)
The alignment of CENH3HCP-3 both prior and after the removal of unreliable regions.
(DOC)
The topologies of the inferred phylogenetic trees of both CENH3HCP-3 and CENP-CHCP-4.
(PDF)
In monocentric organisms with asymmetric meiosis, the kinetochore proteins, such as CENH3 and CENP-C, evolve adaptively to counterbalance the deleterious effects of centromere drive, which is caused by the expansion of centromeric satellite repeats. The selection regimes that act on CENH3 and CENP-C genes have not been analyzed in organisms with ho...
Diffuse large B-cell lymphoma (DLBCL) is the most frequent lymphoma in adults. There are specific alterations that appear repeatedly in DLBCL cases and play a role in lymphomagenesis or progression of the disease. Some aberrations were used as prognostic markers in the pre-rituximab era. Addition of rituximab to the classical anthracycline-based ch...
This paper describes a modified algorithm for inferring phylogenetic trees based on distance techniques. The input of the
algorithm consists of predefined clusters of data. It uses a usual agglomerative approach, however it involves a novel technique
for distance matrix creation as the task of clustering predefined groups of human mitochondrial DNA...
Chromosome numbers were determined for 97 samples of 95 sedge taxa (Carex) from the following countries: Austria (6 records), Bulgaria (1), the Canary Islands (Spain, 1), Cape Verde (1), the Czech Republic (51), Hungary (1), Italy (2), Norway (8), Russia (15), Slovakia (1), Sweden (1) and 9 North American plants cultivated in Czech botanical garden...
Transposable elements (TEs) are considered to be an important source of genome size variation and genetic and phenotypic plasticity in eukaryotes. Most of our knowledge about TEs comes from large genomic projects and studies focused on model organisms. However, TE dynamics among related taxa from natural populations and the role of TEs at the speci...
Concatenated alignment of consensus sequences for ITS and ppc. The alignment used for the construction of the phylogenetic tree for the analyzed species. Sequence identification: copEmam13-cop (Ty1-copia), E (Eleocharis), mam (first three letters of species name), 13 (number of clone).
Alignment of Ty3-gypsy sequences. The alignment used for the construction of the phylogenetic tree of Ty3-gypsy sequences. Sequence identification: gypEaus27-gyp (Ty1-gypsy), E (Eleocharis), aus (first three letters of species name), 27 (number of clone).
Number of sequenced LTR retrotransposon clones per species and their respective GenBank accession numbers
Alignment of Ty1-copia sequences. The alignment used for the construction of the phylogenetic tree of Ty1-copia sequences. Sequence identification: copEmam13-cop (Ty1-copia), E (Eleocharis), mam (first three letters of species name), 13 (number of clone).
Neighbor-joining phylogenetic tree of Ty1-copia. Sequences corresponding to Helos1 are highlighted and depicted in red. Only bootstrap values higher than 50 are shown above branches. Sequence identification: copEmam13-cop (Ty1-copia), E (Eleocharis), mam (first three letters of species name), 13 (number of clone).
Neighbor-joining phylogenetic tree of Ty3-gypsy. Species-specific clades of Eleocharis ovata, E. intersticta, E. cellulosa and E. quinqueflora are highlighted and depicted in blue. Only bootstrap values higher than 50 are shown below branches. Sequence identification: gypEaus27-gyp (Ty1-gypsy), E (Eleocharis), aus (first three letters of species na...
List of plant samples. The list includes full taxonomic names of analyzed species and their locations, including GPS positions, names of collectors and dates of collections.
Projects
Projects (3)
A potential causal link between the size of chromosomes and their kinetochores would provide space for centromere drive (or other mechanisms able to change the kinetochore size) to propel the evolution of entire chromosomes and genomes. We are interested in whether the size relation between chromosomes and their functional centromeres really exists and, if so, whether the chromosomes/genome size evolution in clades with potential for centromere drive differs from clades without it.
Holocentric chromosomes, as a structural alternative to monocentric chromosomes, have evolved independently many times in Eukaryotes. Since only advantageous traits originate repeatedly in evolution, the aim of our project is to reveal such an advantage of holocentrism which is only possible by comparing holo- to monocentrics. We will analyze species and phylogenetic diversity of the largest holocentric clade of flowering plants (Cyperaceae+Juncaceae) relative to very similar, but monocentric Poaceae on a global latitudinal gradient of UV-B radiation, whose increased tolerance should be the key to the success of holocentrism. We will also analyze their competition, reaction to UV-B stress (endopolyploidy, flavonoids content), germination and survival on altitudinal UV-B gradients in nature and controlled experiments in climatic chambers. Using GBIF data, we also intend to compare the largest holocentric clade of animals (Lepidoptera) to related insect monocentric lineages.
The main goal of the project is to assess the conditions under which holocentric species better germinate, survive and compete with their monocentric relatives and to what extent such an advantage at individual or population level affects evolutionary success of whole holocentric clades compared to related monocentric clades.
An adaptive origin of holocentric chromosomes (without localized centromere) as a defense against centromere drive is analyzed using selection regimes acting on kinetochore proteins. To explain surprisingly negative 2C/2n correlation and extreme divergences in holocentric chromosome sizes and numbers we propose a new evolutionary mechanism of “holokinetic drive” that will be tested by the study of segregation ratio of fragmented/non-fragmented homologs in the progeny of structural heterozygotes prepared via x-irradiation. Genome size, genomic GC%, portions and rates of particular modes of karyotype evolution (aneuploidy, polyploidy, chromosomal fusion/fission and repetitive DNA proliferation/removal) will be analyzed in holocentrics (Cyperaceae+Juncaceae, Chionographideae, Cuscuta subg. Cuscuta and Grammica, Drosera) and their sister monocentric clades using flow cytometry, chromosome counting and newly developed phylogenetic algorithm. A new detection technique combining irradiation and flow cytometry was developed for an effective screening for holocentrism in plants. The project is supported by Czech Science Foundation under registration number 13-29362S.