Karol Krak

Karol Krak
Czech University of Life Sciences, Prague, Czech Republic

PhD

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76
Publications
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Publications

Publications (76)
Article
Full-text available
The diploid A. glutinosa (L.) Gaertn. is widespread throughout the European continent, except in the Iberian and Balkan Peninsulas where tetraploid populations have been discovered. We focused on the tetraploid species described as A. rohlenae Vít, Douda and Mandák that occupies the western part of the Balkan Peninsula, where it has likely complete...
Article
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Background: CACTA transposable elements (TEs) comprise one of the most abundant superfamilies of Class 2 (cut-and-paste) transposons. Over recent decades, CACTA elements were widely identified in species from the plant, fungi, and animal kingdoms, but sufficiently studied in the genomes of only a few model species although non-model genomes can bri...
Article
The efficient uptake of nutrients depends on the ability of roots to respond to gradients of these resources. While pot experiments have shown that species differ in their ability to proliferate their roots in nutrient‐rich patches, the role of such differences in determining root shapes in the field is unclear. We used fine‐scale qPCR‐based specie...
Article
Full-text available
Nuclear ribosomal DNA (nrDNA) has displayed extraordinary dynamics during the evolution of plant species. However, the patterns and evolutionary significance of nrDNA array expansion or contraction are still relatively unknown. Moreover, only little is known of the fate of minority nrDNA copies acquired between species via horizontal transfer. The...
Article
Intra‐specific variability is a cornerstone of evolutionary success of species. Acquiring genetic material from distant sources is an important adaptive mechanism in bacteria, but it can also play a role in eukaryotes. In this paper we investigate the nature and evolution of chromosomal segment of panicoid (Poaceae, Panicoideae) origin occurring in...
Article
Full-text available
Satellite DNA (satDNA) is one of the major fractions of the eukaryotic nuclear genome. Highly variable satDNA is involved in various genome functions, and a clear link between satellites and phenotypes exists in a wide range of organisms. However, little is known about the origin and temporal dynamics of satDNA. The "library hypothesis" indicates t...
Article
Full-text available
Diploid Alnus glutinosa s. str. and autotetraploid A. rohlenae form a narrow hybrid zone in a study area in southern Serbia, which results in triploid hybrid formation. The vast majority of previous studies have been focused on studies of maternal plants, but the offspring resulting from their crossing have not been much studied. Here, we use the v...
Article
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Extensive and complex links exist between transposable elements (TEs) and satellite DNA (satDNA), which are the two largest fractions of eukaryotic genome. These relationships have a crucial effect on genome structure, function and evolution. Here, we report a novel case of mutual relationships between TEs and satDNA. In the genomes of Chenopodium...
Article
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Roots are capable of strong plastic responses to environmental signals, but the extent of such responses in the field is essentially unknown. Here, we aimed to identify interspecific root aggregations and segregations as indicators of plastic responses to the presence of other species. Furthermore, we asked whether aggregations change with heteroge...
Article
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Premise: A set of polymorphic nuclear microsatellite loci was developed and tested for use in population genetic analyses of Anthericum ramosum (Agavaceae) and related species. Methods and results: Sequences of 110 primers were extracted in silico from Illumina MiSeq genome skimming data. The degree of polymorphism of 19 loci was tested in four...
Article
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Premise: Microsatellite markers were developed for the perennial herb Salvia pratensis (Lamiaceae), a species representative of European dry grasslands. The development of microsatellite markers is needed for genetic and phylogeographical studies of species from the genus Salvia. Methods and results: We used low-coverage Illumina sequencing to i...
Article
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Polyploidization, a key driver of plant diversification, is believed to have interacted with Pleistocene climatic oscillations and local ecological factors, leading to a complex spatio-ecological mosaic of diploid and polyploid populations. The typical ecogeographic pattern in European plants involves spatially restricted diploids growing in southe...
Article
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Premise: Polymorphic microsatellite markers were developed as a tool for genetic investigations of Filipendula vulgaris (Rosaceae) and related species. Methods and results: Seventeen new polymorphic microsatellite markers were developed for F. vulgaris using the Illumina MiSeq platform. Polymorphism of the 17 loci was tested in three populations...
Article
The centre‐periphery hypothesis (CPH) predicts a decrease in population performance from the centre of the species range towards the edge, hindering further species expansion. To overcome ecological limitation, local adaptation of peripheral populations is assumed necessary to extend niche space and thus to potentially facilitate species’ range exp...
Article
The Holocene history of annual plant species is at best shadowy because, for most, the palaeobotanical data are scarce or absent. Hence, there is limited information on their glacial refugia and postglacial colonization pathways. Also, little is known on how human activity has affected their expansion. Here, we outline the joint influences of postg...
Article
Full-text available
Satellite DNA (satDNA) is the most variable fraction of the eukaryotic genome. Related species share a common ancestral satDNA library and changing of any library component in a particular lineage results in interspecific differences. Although the general developmental trend is clear, our knowledge of the origin and dynamics of satDNAs is still fra...
Data
Supplementary data 1. Occurrence of CficCl-61-40 satDNA family in genomes of Chenopodium diploid species revealed by RepeatExplorer pipeline and formations of high order repeat (HOR) units
Data
Supplementary data 3. Repetitive elements selected for sequence characterization and in situ hybridization and primers used for amplification.
Data
Reconstruction of the major part of the ancestral monomer BLAST-detected relatedness between minisatellite monomers of CficCl-61-40 satDNA family makes it possible to determine the major part of the ancient monomer. For this reconstruction for one RE cluster of C. bryobifolium (cluster 2) and for seven RE clusters C. vulvaria (clusters 28, 94, 112,...
Data
Chromosomal distribution CficCl-61-40 satDNA family sequences. CficCl-61-40 is labelled red; C. acuminatum-specific HOR unit CacuCl-1-117 of 117 bp is labelled green.
Data
N). For these monomers the sequence alignments containing the consensus sequence reconstructed by RE and sequences obtained by cloning and sequencing of clones are presented. For the cloned sequences identities with the consensus is represented by dots, differences by the alternative nucleotide characters. Tables contain the % of sequence similarit...
Article
Aim We hypothesised that during the Holocene, the distributions of species such as crop weeds have been significantly influenced by human activity. We aimed to (a) identify the main centres of diversity of the Chenopodium album agg. species and (b) test if these species colonised Europe from western Asia, most likely due to the westward expansion o...
Article
Using flow cytometry we explored the cytogeography of Seseli libanotis (Apiaceae) from central Europe and several adjacent areas. We detected diploids and tetraploids, but no triploids. Diploids are distributed across nearly all study areas, whereas tetraploids occur in Czechia, the Pannonian lowlands of northeastern Austria and western Slovakia, i...
Article
Hybridization and polyploidization represent an important speciation mechanism in the diploid-polyploid complex of the Chenopodium album aggregate. In the present study we successfully reconstructed the evolutionary histories of the majority of Eurasian representatives of the C. album aggregate, resulting in the most comprehensive phylogenetic anal...
Article
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• Premise of the study: Microsatellite primers were developed to characterize the genetic diversity and structure of the annual herb Atriplex tatarica (Amaranthaceae) and to facilitate ecological and evolutionary studies of A. tatarica and its relatives. • Methods and Results: Sixteen novel microsatellite primers were developed for A. tatarica bas...
Article
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Inoculation with arbuscular mycorrhizal fungi (AMF) may improve plant performance at disturbed sites, but inoculation may also suppress root colonization by native AMF and decrease the diversity of the root-colonizing AMF community. This has been shown for the roots of directly inoculated plants, but little is known about the stability of inoculati...
Data
Root colonization of the experimental plants. (PDF)
Data
Variation in the abundance of the inoculant R. irregularis Chomutov. (PDF)
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Variation in Pielou's evenness index J', abundance of Rhizophagus irregularis and the sum of abundances of other AMF taxa. (PDF)
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Variation in the abundances of C. claroideum, 'uncultured Glomeraceae' and F. mosseae. (PDF)
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Total dry weights of M. sativa and P. arundinacea D seedlings at planting into the experiment. (PDF)
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Numbers of evaluated replicates per experimental treatment. (PDF)
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Real-time PCR assays in mitochondrial ribosomal DNA. (PDF)
Data
Characterization of the diversity of native arbuscular mycorrhizal fungi. (PDF)
Data
Real-time PCR assays in nuclear ribosomal DNA. (PDF)
Data
Variation in the proportion of the inoculant and the abundance of native R. irregularis. (PDF)
Data
Abundances of native R. irregularis and inoculated R. irregularis Chomutov. (PDF)
Data
Abundances of C. claroideum, 'uncultured Glomeraceae' and F. mosseae. (PDF)
Data
Phylogenetic analysis of the native arbuscular mycorrhizal fungal community. (PDF)
Data
Phylogenetic analysis of Rhizophagus irregularis haplotypes. (PDF)
Data
Variation in root colonization. (PDF)
Article
Vertical differentiation in root placement is one of the potential mechanisms of plant niche differentiation. It can be due to the remarkable plasticity of roots in response to nutrients and neighbours, but most data on it come from pot or garden experiments. The roles of vertical differentiation and of plasticity in it in the field are thus not we...
Article
Full-text available
In the present study, we investigate the variation of European representatives of Alnus subg. Alnus, i.e., Alnus glutinosa and A. incana, in Europe and partly North Africa. Four distinct Alnus taxa were recognized using a multidisciplinary approach based on multivariate morphometrics, karyology, flow cytometry and nuclear microsatellite analyses. B...
Article
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Background and aims: Knowledge of diploid phylogeny and ecogeography provide a foundation for understanding plant evolutionary history, diversification patterns and taxonomy. The genus Anthoxanthum (vernal grasses, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and poorly resolved evolutionary relat...
Article
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The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley (Hordeum) species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panico...
Article
The significance of the wide interspecific variation in nuclear genome size of angiosperms is still not fully understood. It has been repeatedly suggested, however, that genome size can impose phenotypic constraints on plant development, phenology and ecological performance. We analysed nuclear genome size variation in diploid and polyploid species...
Article
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Reticulate evolution is characterized by occasional hybridization between two species, creating a network of closely related taxa below and at the species level. In the present research, we aimed to verify the hypothesis of the allopolyploid origin of hexaploid C. album s. str., identify its putative parents and estimate the frequency of allopolypl...
Article
Tremendous interspecific genome size variation is a well known phenomenon, whereas genome size within a species is supposed to be exceptionally stable and thus useful as a taxonomic trait. Using DAPI flow cytometry, we tested the stability of genome size in various representatives of Chenopodium s.s. (Amaranthaceae) across a broad geographical rang...
Article
Full-text available
We reconstructed the historical pattern of postglacial biogeographic range expansion of the boreal tree species Alnus incana in Europe. To assess population genetic structure and diversity, we performed a combined analysis of nuclear microsatellite loci and chloroplast DNA sequences (65 populations, 1004 individuals). Analysis of haplotype and micr...
Article
Background and aims: Polyploidy in plants has been studied extensively. In many groups, two or more cytotypes represent separate biological entities with distinct distributions, histories and ecology. This study examines the distribution and origins of cytotypes of Alnus glutinosa in Europe, North Africa and western Asia. Methods: A combined app...
Article
Genetic admixture is supposed to be an important trigger of species expansions because it can create the potential for selection of genotypes suitable for new climatic conditions. Up until now, however, no continent-wide population genetic study has performed a detailed reconstruction of admixture events during natural species expansions. To fill t...
Article
Full-text available
Premise of the study: Microsatellite markers were developed for the Pilosella alpicola group (Asteraceae), comprising four closely related species distributed in subalpine areas of Europe. These species are believed to have diverged recently, but display contrasting cytogeographic patterns and variation in breeding systems, representing a promising...
Article
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We investigated 39 previously developed Betula, Alnus, and Corylus simple sequence repeat (SSR) markers for their utility in the cross-generic amplification of two European alder species, i.e., Alnus glutinosa and A. incana. Of these markers, ten loci had successful amplification within Alnus species. Finally, we designed two multiplexes composed o...
Article
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Background and Aims Recently formed allopolyploid species represent excellent subjects for exploring early stages of polyploid evolution. The hexaploid Cardamine schulzii was regarded as one of the few nascent allopolyploid species formed within the past ∼150 years that presumably arose by autopolyploidization of a triploid hybrid, C. × insueta; ho...
Article
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Background/aims: Recently, new palaeoecological records supported by molecular analyses and palaeodistributional modelling have provided more comprehensive insights into plant behaviour during the last Quaternary cycle. We reviewed the migration history of species of subgenus Alnus during the last 50,000 years in Europe with a focus on (1) a gener...
Article
Full-text available
Communities of arbuscular mycorrhizal fungi (AMF) are crucial for promoting plant productivity in most terrestrial systems, including anthropogenically managed ecosystems. Application of AMF inocula has therefore become a widespread practice. It is, however, pertinent to understand the mechanisms that govern AMF community composition and their perf...
Article
Full-text available
Phylogeny reconstruction based on multiple unlinked markers is often hampered by incongruent gene trees, especially in closely related species complexes with high degrees of hybridization and polyploidy. To investigate the particular strengths and limitations of chloroplast DNA (cpDNA), low-copy nuclear and multicopy nuclear markers for elucidating...
Article
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Curcuma comprises 120 species that occur throughout tropical and subtropical Asia. The taxonomy of the genus is haunted by polyploid speciation and homoploid hybridization, making it the most challenging genus in Zingibereae (Zingiberaceae). Curcuma is best known for turmeric (C. longa), but numerous species are extensively used as medicinal plants...
Article
Full-text available
Real-time PCR in nuclear ribosomal DNA (nrDNA) is becoming a well-established tool for the quantification of arbuscular mycorrhizal (AM) fungi, but this genomic region does not allow the specific amplification of closely related genotypes. The large subunit of mitochondrial DNA (mtDNA) has a higher-resolution power, but mtDNA-based quantification h...