Head: Ing. Mgr. Pavel Trávníček, Ph.D.
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Research topics
- Investigation of individual genomes (horizontal gene transfer, DNA endoreduplication, cytogenetics)
- Studying of micro-evolutionary processes at the population level (cytotypes interaction, phylogeography, etc.)
- Unraveling species-level interactions (evolution of diploid-polyploid complexes, hybrid speciation, molecular systematics, etc.)
- Detection of evolutionary forces acting at supra-generic level (e.g., causes of differential radiation at generic and higher levels)
- Biosystematics of polyploid complexes
- Ecological differentiation of closely related species
Selected recent results
1/ Ancient hybridization in Curcuma (Zingiberaceae) – Accelerator or brake in lineage diversifications?
Hybridization is a widespread phenomenon in the evolution of plants and exploring its role is crucial to understanding diversification processes of many taxonomic groups. Recently, attention is focused on the role of ancient hybridization that may be trigger of evolutionary radiation or can prevent further diversification. The causes, frequency, and consequences of ancient hybridization remain to be explored. Here, we present an account of several events of ancient hybridization in the economically important plant genus Curcuma (Zingiberaceae), which harbors about 130 known species. We analyzed 1094 targeted nDNA genes and plastomes obtained by next-generation sequencing of 37 species, representing the known genetic diversity and spanning the geographical distribution of the genus. Using phylogenetic network analysis, we show that the entire genus as well some of its lineages arose via introgression. We also document a single event of ancient hybridization, that represents an evolutionary dead end. We discuss distinct circumstances of those hybridization events that deal mainly with (in)congruence in chromosome counts of the parental lineages.
- Skopalíková J., Leong-Škorničková J., Šída O., Newman M., Chumová Z., Zeisek V., Jarolímová V., Dalberg Poulsen A., Dantas-Queiroz M. V., Fér T. & Záveská E. 2023: Ancient hybridization in Curcuma (Zingiberaceae) – Accelerator or brake in lineage diversifications? Plant Journal 116, 773 – 785. https://doi.org/10.1111/tpj.16408
Turmeric (Curcuma longa) – the best-known and most economically important species of the genus Curcuma, whose evolutionary history was influenced by ancient hybridization.
2/ Telomere sequence variability in genotypes from natural plant populations: unusual block-organized double-monomer terminal telomeric arrays
The paper explores telomere sequence variability in natural plant populations, focusing on four Chenopodium species. Utilizing Oxford Nanopore sequencing and fluorescent in situ hybridization, the study reveals significant variation in the structure and chromosomal distribution of telomeric sequences. Notably, it identifies block-organized double-monomer telomeres, where Arabidopsis-type motifs (TTTAGGG) are interspersed with derivative motifs (TTTAAAA). These findings indicate that variations in telomeric sequences may contribute to genomic variability in plants. The paper proposes two models for the formation of these derivative monomers and highlights the importance of non-canonical telomeric arrays in driving genomic diversity in natural environments.
- Belyayev A., Kalendar R., Josefiová J., Paštová L., Habibi F., Mahelka V., Mandák B. & Krak K. 2023: Telomere sequence variability in genotypes from natural plant populations: unusual block-organized double-monomer terminal telomeric arrays. BMC Genomics 24, 1 – 11. doi:1186/s12864-023-09657-y
Fluorescent in situ hybridization of the two telomeric repeat sequences of Chenopodium iljinii. Arabidopsis-type (TTTAGGG) – red color and the derived sequence (TTTAAAA) – green color. Green arrows indicate the position of combined TTTAGGG+TTTAAAA sequence arrays.
3/ Relationship between transposons and ecology in the genus Pteronia
As part of the Cape flora research, we have focused on the genus Pteronia (Asteraceae), which represents one of the highly diversified endemic genera of the local flora. In the first phase, based on a broad screening of ca 60 representatives of the genus, we identified 31 diploid species, in which significant variation in genome size was detected. For these species, we reconstructed phylogenetic relationships using targeted enrichment of specific DNA fragments using Illumina sequencing. The same samples were also used for low-coverage whole-genome sequencing to obtain qualitative and quantitative information on repetitive genomic elements (transposons, satellite DNA, etc.) for comparative analysis. Our results showed that the change in genome size is associated with a rapid increase in Tekay elements from the Ty3-gypsy family and is exclusively linked to those species that grow only in the fynbos (specific Mediterranean-type vegetation of the Cape region). It can be hypothesized that the increase in genome size associated with a significant accumulation of Tekay elements is closely linked to the transition of species originally adapted to the arid vegetation of the succulent karoo to the fynbos.
- Chumová Z., Belyayev A., Mandáková T., Zeisek V., Hodková E., Šemberová K., Euston-Brown D. & Trávníček P. 2022: The relationship between transposable elements and ecological niches in the Greater Cape Floristic Region: A study on the genus Pteronia (Asteraceae). Frontiers in Plant Science 13, 1 – 18. doi: 3389/fpls.2022.982852
Phylogeny of species of the genus Pteronia with identified satellite DNA families. (A) ASTRAL species tree of the genus Pteronia based on 244 nuclear COS loci with genome size evolution. (B-D) Localization of chromosomes of satellite families 1 (green), 2 (red) and 4 (magenta) shown in P. unguiculata (B), P. ovalifolia (C) and P. incana (D).
4/ CACTA transposons in the genus Chenopodium
CACTA transposable elements (TEs) comprise one of the most abundant superfamilies of Class 2 (cut-and-paste) transposons. We used low coverage genome sequencing and short-read based assembly algorithms to detected complete CACTA elements in 22 Chenopodium album aggregate species for determination of their diversity.
We revealed a structural variation of CACTA elements. We identified altogether four types of these repetitive elements differing by the number and combination of conserved protein domains. In some species two coexisting types of CACTA elements were found. In some elements we identified captured fragments of flowering related genes. Database analyses showed that these structural variants of CACTA element are widely scattered across the phylogenetic tree of Angiosperms.
Our study demonstrated that while CACTA transposons preserve an elementary structure a wide range of additional structural modifications involving both coding and non-coding sequence, occur to these elements in plant genomes. Modified CACTA elements may gain novel functional features and impact therefore evolutionary trajectory of the host genome.
- Belyayev A., Josefiová J., Jandová M., Kalendar R., Mahelka V., Mandák B. & Krak K. 2022: The structural diversity of CACTA transposons in genomes of Chenopodium (Amaranthaceae, Caryophyllales) species: specific traits and comparison with the similar elements of angiosperms. Mobile DNA 13, 1 – 16. doi:1186/s13100-022-00265-3
A) Schematic representation of the four different structural variants of the CACTA elements. Colored rectangles represent the different conserved protein domains. B) Distribution of the four different CACTA element types in angiosperms. Occurrence of the particular type is indicated by colored asterisks. Carophyllales, the group comprising Chenopodium is highlighted by red.
5/ A Panicum-derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress-related genes
The evolution of the genus Hordeum is associated with multiple horizontal transfers of genetic material from panicoid grasses. One of the transfers, and probably the oldest, can be characterized as the transfer of DNA from a representative of the genus Panicum to the genome of the ancestor of Hordeum’s section Stenostachys. The object of transfer was probably a set of fragments of chromosomes from Panicum, which were rearranged into one foreign fragment in the present genomes of wild barleys. The fragment contains several protein-coding genes, as well as ribosomal DNA and transposable elements. Panicoid protein-coding genes play a role in stress conditions, with at least one appearing to be potentially functional in present Hordeum species. Horizontal transfer could thus play a role in the adaptation of Hordeum to a changing environment.
- Mahelka V., Krak K., Fehrer J., Caklová P., Nagy Nejedlá M., Čegan R., Kopecký D. & Šafář J. 2021: A Panicum-derived chromosomal segment captured by Hordeum a few million years ago preserves a set of stress-related genes. Plant Journal 105, 1141 – 1164. doi:10.1111/tpj.15167
Hordeum (wild barley) species carry a chromosomal segment that was obtained from Panicum. Whereas the lineages of pooid and panicoid grasses split about 50 million years ago, the Panicum-like DNA fragment in Hordeum was obtained by horizontal gene transfer between 2.9 and 1.7 million years ago. The fragment contains protein-coding genes, ribosomal DNA genes (rDNA) and transposable elements (TEs). Before integration in Hordeum, different Panicum-like DNA fragments were rearranged into a single locus. At least one of the genes is potentially functional.
6/ Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids
Using the Pleurothallidinae as a model orchid group, we attempted to assess the role of repetitive DNA replication, chromosomal variation and endoreplication type in the evolution of genome size. Indeed, orchids are the only plant group in which a unique type of endoreplication is known, where only a species-specific part of the genome is duplicated during cell differentiation. Our research has shown that partial endoreplication leads to preferential replication of functional parts of the genome (e.g. genes). In contrast, parts of the genome rich in repetitive sequences, i.e. those that do not encode genes and thus do not manifest themselves in the characteristics of organisms, do not replicate during endoreplication. Furthermore, we have shown that genome evolution at the species level proceeds at a double rate: while the coding part of the genome is more or less constant in closely related species, the part of DNA containing non-coding regions is constantly changing, and with it the overall size of the genome. This leads, among other things, to a huge variation in genome size in orchids.
- Chumová Z., Záveská E., Hloušková P., Ponert J., Schmidt P.-A., Čertner M., Mandáková T. & Trávníček P. 2021: Repeat proliferation and partial endoreplication jointly shape the patterns of genome size evolution in orchids. Plant Journal 107, 511 – 524. doi:10.1111/tpj.15306
Images of flowers of representatives of the orchid group Pleurothaliidinae, ordered from the basalmost (bottom right) to the most derived (top left). The unusual morphological diversity is accompanied by a unique genomic feature, previously undiscovered in organisms other than orchids, which has a major impact on their evolution of genome size.
7/ The major satellite DNA families of the diploid Chenopodium album aggregate species: Arguments for and against the “library hypothesis”
Popis anglicky: Satellite DNA (satDNA) is one of the major fractions of the eukaryotic nuclear genome, however still little is known about its origin and temporal dynamics. The “library hypothesis” indicates that the rapid evolutionary changes experienced by satDNAs are mostly quantitative. Although this hypothesis has received some confirmation, a number of its aspects are still controversial. Here we address this hypothesis using next-generation sequencing based analysis of repeatome for diploid species representing the major evolutionary lineages of Chenopodium album aggregate. We identified eight satDNA families with highly variable distribution among these lineages. We found that new satDNA families may arise or existing ones may be eliminated even during short periods of evolution. Thus our data refute the “library hypothesis”, rather than confirming it, and in our opinion, it is more appropriate to speak about “the library of the mechanisms of origin”.
Chromosomal distribution of eight satDNA families. (A) FISH with the f1 probe on chromosomes of C. acuminatum. (B) FISH with the f2 probe on chromosomes of C. acuminatum. (C) FISH with the f3 probe on chromosomes of C. suecicum. (D) FISH with the f4 probe on chromosomes of C. suecicum. (E) FISH with the f5 probe on chromosomes of C. suecicum. (F) FISH with the f6 probe on chromosomes of C. acuminatum. (G) FISH with the f7 probe on chromosomes of C. acuminatum. An enlarged chromosome with a clear centromeric signal is shown in a separate box. (H) FISH with the f8 probe on chromosomes of C. iljinii. A metaphase plate with a red signal from the f8 satDNA family is shown on the left, and DAPI staining of the same metaphase plate is shown on the right. The smallest pair of chromosomes with major blocks is indicated by arrows. (I) FISH with a microsatellite probe on chromosomes of C. acuminatum. All chromosomes were counterstained with DAPI. Bars represent 5 µm.
- Belyayev A., Jandová M., Josefiová J., Kalendar R., Mahelka V., Mandák B. & Krak K. (2020): The major satellite DNA families of the diploid Chenopodium album aggregate species: Arguments for and against the “library hypothesis”. – PLoS ONE 15(10). doi: 10.1371/journal.pone.0241206
8/ Populations of Pilosella species in ruderal habitats in the city of Prague: consequences of the spread of P. aurantiaca and P. rothiana
Taxa of the genus Pilosella were documented on three ruderal sites of south and west Prague periphery. The study was aimed namely to recent hybridization, ploidy level/chromosome counts and mode of reproduction. Up to 18 Pilosella taxa were found co-occurring in single locality, most of them sterile or partially fertile hybrids, than with production of polyhaploid offspring. Nevertheless, it seems to be likely that those hybrid swarms will be stabilized via apomixis in course of time. Due to the very recent coexistence of taxa, which have not yet usually grown together, most of the hybrids observed have been undescribed.
Although Pilosella fuscoatra is a hybrid between two apomictic parents, two clones with different colors and modes of reproduction (apomictic and sexual) were found at the locality of Hrnčíře.
- Krahulec F., Krahulcová A., Urfus T. & Doležal J. (2020): Populations of Pilosella species in ruderal habitats in the city of Prague: consequences of the spread of aurantiaca and P. rothiana. – Preslia 92: 167–190. doi: 10.23855/preslia.2020.167
9/ Analyses of hybrid viability across a hybrid zone between two Alnus species using microsatellites and cpDNA markers
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 tension zone model seems to offer the most adequate explanation of our observations, with selection against triploid hybrids and the spatial positioning of the hybrid zone. Despite selection against them, the triploid hybrids play an important role in the exchange of genes between the two species and therefore serve as a bridge for introgression. The presence of fertile triploids is essential for enriching the haplotype diversity between these species and for the development of new genetic lineages.
Diploid Alnus glutinosa s. str. and autotetraploid A. rohlenae form a narrow hybrid zone in southern Serbia, which results in triploid hybrid formation. The triploid hybrids play an important role in the exchange of genes between the two species and therefore serve as a bridge for introgression. Typical locality on hybrid zone of the two species in Serbia.
- Šmíd J., Douda J., Krak K. & Mandák B. (2020): Analyses of hybrid viability across a hybrid zone between two Alnus species using microsatellites and cpDNA markers. – Genes 11(7):770. doi: 10.3390/genes11070770
10/ The adaptive potential of genome doubling depends on local environmental conditions
While it has been repeatedly shown that polyploidization has direct effect on plant phenotype, the adaptive potential of ploidy-induced phenotypic novelty remained unclear. For our study, we selected a unique model system consisting of diploids and recently derived autotetraploids co-occurring in natural populations of the serpentine tolerant plant Knautia serpentinicola. Di- and tetraploid individuals were cultivated from seeds in a common garden experiment under experimental setting simulating two major environmental factors affecting plant life at the natural locality (presence / absence of serpentine substrate and interspecific competition). We have shown that tetraploids attained significantly higher values of both above- and below-ground biomass compared to their diploid progenitors. Interestingly, the tetraploid superiority in vegetative fitness indicators was most prominent when they were cultivated together with a competitor in nutrient-rich substrate. This suggests that provided there are sufficient nutrients, tetraploids can be more successful in tolerating interspecific competition than their diploid progenitors. Such fitness advantage could promote the establishment of newly originated polyploids by allowing them to colonize new microhabitats, which was indeed observed at the natural site.
Experimental cultivation has shown that tetraploids of Knautia serpentinicola exhibit higher fitness than their diploid progenitors, especially when cultivated in nutrient-rich substrate with an interspecific competitor (grass Agrostis capillaris). Photo by M. Čertner
- Čertner M., Sudová R., Weiser M., Suda J. & Kolář F. (2019). Ploidy-altered phenotype interacts with local environment and may enhance polyploid establishment in Knautia serpentinicola (Caprifoliaceae). New Phytologist 221: 1117-1127. doi: 10.1111/nph.15426
11/ Diversity in genome size and GC content shows adaptive potential in orchids and is closely linked to partial endoreplication, plant life-history traits and climatic conditions
(In cooperation with University of South Bohemia in České Budějovice.)
Genome size is thoroughly studied in seed plants because it exhibits huge variation spanning 2400-fold difference and is suspected to play an important role in their evolution. Although the GC content varies significantly less, it is thought to be important for the ability of plants to adapt to extreme climatic conditions. Cosmopolitan groups of plants, such as orchids, are therefore a suitable model system for identifying the evolutionary significance and adaptive role of genome size and GC content. Diversity in both traits possesses substantial adaptive potential in orchids and is closely linked to the ability to replicate DNA partially throughout the cell differentiation, to particular life-history traits, and climatic conditions. It means, for example, differential evolution of genome size for geophytes of temperate climatic zones or epiphytes of tropical regions. Thus, obvious trends in trait evolution to different optima under different conditions are characteristic for orchids. Namely GC content exhibits unparalleled diversity and orchids set new limits for angiosperms as well as for eucaryotes. The immense role of partial endoreplication, a unique feature of orchids across living organisms, was detected in shaping the diversity of genome size, and GC content.
Calypso bulbosa var. occidentalis, an orchid geophyte facing extremely short vegetation periods and cold winters, has set a new lowest limit for the estimated GC content of plants (23.9%). Photo by J. Ponert
- Trávníček P., Čertner M., Ponert J., Chumová Z., Jersáková J. & Suda J. (2019). Diversity in genome size and GC content shows adaptive potential in orchids and is closely linked to partial endoreplication, plant life-history traits and climatic conditions. New Phytologist 224: 1642-1656. doi: 10.1111/nph.15996
12/ Polyploid evolution: The ultimate way to grasp the nettle
Polyploidy is one of the major forces of plant evolution and widespread mixed-ploidy species offer an opportunity to evaluate its significance. We therefore selected the cosmopolitan species Urtica dioica (stinging nettle), examined its cytogeography and pattern of absolute genome size, and assessed correlations with bioclimatic and ecogeographic data (latitude, longitude, elevation). We evaluated variation in ploidy level using an extensive dataset of 7012 samples from 1317 populations covering most of the species’ distribution area. The widespread tetraploid cytotype (87%) was strongly prevalent over diploids (13%). A subsequent analysis of absolute genome size proved a uniform Cx-value of core U. dioica (except for U. d. subsp. cypria) whereas other closely related species, namely U. bianorii, U. kioviensis and U. simensis, differed significantly. We detected a positive correlation between relative genome size and longitude and latitude in the complete dataset of European populations and a positive correlation between relative genome size and longitude in a reduced dataset of diploid accessions (the complete dataset of diploids excluding U. d. subsp. kurdistanica). In addition, our data indicate an affinity of most diploids to natural and near-natural habitats and that the tetraploid cytotype and a small part of diploids (population from the Po river basin in northern Italy) tend to inhabit synanthropic sites. To sum up, the pattern of ploidy variation revealed by our study is in many aspects unique to the stinging nettle, being most likely first of all driven by the greater ecological plasticity and invasiveness of the tetraploid cytotype.
Distribution of two dominant cytotypes of stinging nettle (Urtica dioica) in Europe and West Asia. Map of all samples based on flow cytometric analyses of 1305 populations. The size of the circles reflects the number of populations. From Rejlová et al. (2019)
- Rejlová L., Chrtek J., Trávníček P., Lučanová M., Vít P. & Urfus T. (2019). Polyploid evolution: The ultimate way to grasp the nettle. PLoS One 14: 1-24. doi: 10.1371/journal.pone.0218389