František Zedek

Summary: Ferns and angiosperms represent the two largest vascular plant lineages but exhibit striking genomic and ecological contrasts. We investigated whether differences in genome size, chromosome architecture, GC content, and stomatal traits reveal divergent evolutionary trajectories between these lineages. We assembled the most comprehensive dataset to date, integrating genome size, chromosome number and size, GC content, and stomatal traits for over 1100 fern species and compared it with an extensive angiosperm dataset. Ferns exhibited markedly lower variability and c. 16‐fold slower rates of chromosome size evolution than angiosperms. A persistent positive relationship between genome size and chromosome number in ferns suggests limited cytological post‐polyploid diploidization. While ferns generally possess larger stomata, this difference disappears after accounting for genome size, indicating that nucleotypic constraints, rather than lineage‐specific physiology, dictate stomatal dimensions. Both groups share a unimodal GC–genome size relationship peaking at c. 14 Gbp. Larger fern chromosomes imply lower genome‐wide recombination rates, potentially limiting genetic reshuffling and adaptive potential. Our results highlight fundamentally divergent evolutionary trajectories, likely shaped by meiotic symmetry in ferns and meiotic asymmetry, possibly centromere drive, and post‐polyploid diploidization in angiosperms, defining the functional and genomic landscapes of these lineages across deep evolutionary timescales.

Centromere architecture can determine where transposable elements persist, yet its effects on retrotransposon turnover remain poorly understood. Here we test a chromosome-level “nowhere-to-hide” model, in which holocentric chromosomes, owing to distributed centromere activity and reduced chromatin compartmentalization, provide fewer stable repeat-rich refugia than monocentric chromosomes. We combined genome-wide LTR retrotransposon annotation, spatial modelling and FISH across 40 holocentric plant species and 31 closely related monocentric relatives from Poales, Cuscuta , and Melanthiaceae. Overall LTR retrotransposon abundance and Ty1-copia/Ty3-gypsy composition were explained mainly by lineage history and chromosome size, rather than by holocentricity itself. By contrast, element persistence and removal showed dependence on centromere architecture. Intact LTR retrotransposons were younger in holocentric genomes, and holocentric chromosomes lacked the chromosome-size-dependent spatial clustering of element age observed in monocentrics. Solo-LTR profiles further revealed weaker spatial clustering of removal signatures in holocentric chromosomes, consistent with a more homogeneous chromosome-wide landscape of ectopic recombination. Epigenomic analyses of a matched Luzula – Juncus pair indicated that young elements can occur in centromeric chromatin, whereas solo LTRs are associated with more euchromatic contexts. These results support the nowhere-to-hide model, showing that centromere architecture does not shape LTR retrotransposons accumulation, but their persistence and removal efficiency.

Chromosome segregation during cell division relies on the kinetochore, a multiprotein complex that mediates attachment of chromosomes to spindle microtubules. Biophysical considerations predict that kinetochore size should scale with chromosome size to meet increasing mechanical demands during segregation, yet empirical evidence for such scaling within karyotypes remains limited, particularly in species with modest chromosome size variation. Here, we investigated the relationship between chromosome size and kinetochore size in Star of Bethlehem ( Ornithogalum kochii , Asparagaceae), a species from a genus with moderate intra‐karyotype chromosome size variation (2.4–4.5‐fold). Using immunolabelling of the conserved outer kinetochore protein KNL1 and linear mixed‐effects modelling, we analysed 172 chromosomes across multiple metaphases, slides and individuals. We detected a strong positive scaling relationship between chromosome size and kinetochore size, demonstrating that cytogenetic approaches can resolve chromosome–kinetochore scaling even across relatively narrow size gradients. Our results demonstrate that kinetochore size scales with chromosome size even in species with modest intra‐karyotype chromosome size variation, supporting the generality of chromosome–kinetochore scaling. Together with evidence from taxa exhibiting more extreme karyotype heterogeneity, this pattern suggests that centromere and kinetochore architecture is shaped by both functional constraints on chromosome segregation and long‐term evolutionary processes such as centromere drive. Viewed in a broader context, chromosome–kinetochore scaling may also be relevant for processes beyond segregation, as evolutionary changes in centromere and kinetochore architecture could indirectly influence recombination rates through their effects on chromosome size.

Recombination is a fundamental evolutionary process essential for generating genetic diversity, facilitating adaptation, and driving speciation. However, direct measurement of recombination rate remains challenging, as standard methods—such as chiasma counts or genetic linkage maps—are labor intensive and often infeasible for nonmodel species. In this study, we identify chromosome number and mean chromosome size as practical proxies for genome-wide recombination rate by analyzing genetic map data from 73 insect species and supplementary analyses of 157 monocentric flowering plants. We confirm the long-standing hypothesis that monocentric species have nearly twice as many crossovers per chromosome as holocentric species, reflecting structural constraints imposed by diffuse centromeres. Using both ordinary and phylogenetically informed Bayesian regression models, we show that recombination rate increases with chromosome number and decreases with mean chromosome size. Crucially, mean chromosome size is a significantly better predictor, particularly in holocentric species. This insight enables recombination rate estimation in thousands of species with known chromosome sizes, thereby allowing hypothesis testing at scales previously unattainable. Building on these results, we present predictive models applicable to poorly studied holocentric plants. Overall, our study highlights the pivotal role of chromosome architecture in recombination evolution and provides an accessible framework for evolutionary genomic research across diverse lineages.

Recombination is a fundamental evolutionary process essential for generating genetic diversity, facilitating adaptation, and driving speciation. However, direct measurement of recombination rate remains challenging, as standard methods—such as chiasma counts or genetic linkage maps—are labor-intensive and often infeasible for non-model species. In this study, we identify chromosome number and mean chromosome size as practical proxies for genome-wide recombination rate by analyzing genetic map data from 73 insect species and supplementary analyses of 157 monocentric flowering plants. We confirm the long-standing hypothesis that monocentric species have nearly twice as many crossovers per chromosome as holocentric species, reflecting structural constraints imposed by diffuse centromeres. Using both ordinary and phylogenetically informed Bayesian regression models, we show that recombination rate increases with chromosome number and decreases with mean chromosome size. Crucially, mean chromosome size is a significantly better predictor, particularly in holocentric species. This insight enables recombination rate estimation in thousands of species with known genome and chromosome sizes, thereby allowing hypothesis testing at scales previously unattainable. Building on these results, we present predictive models applicable to poorly studied holocentric plants. Overall, our study highlights the pivotal role of chromosome architecture in recombination evolution and provides an accessible framework for evolutionary genomic research across diverse lineages. Article summary: Why do some species have more genetic shuffling than others? We investigated 73 insect species with detailed genetic maps and found that mean chromosome size is the best predictor of genome-wide recombination rate, not the number of chromosomes. This means we can now estimate recombination rates even in species where genetic maps are unavailable, using only genome size and chromosome number. We also show that chromosome structure matters—species with a single centromere per chromosome (monocentric) have nearly double the recombination compared to those with diffuse centromeres (holocentric). These insights open new doors for studying evolution across many organisms.

Moreyra and co-authors, in their recent paper published in Plants, presented a desperately needed Hyb-Seq phylogeny of the genus Cirsium sensu lato. Through their findings, they provided a critical assessment of an earlier proposal of ours to separate Cirsium sect. Eriolepis and Cirsium italicum into the genera Lophiolepis and Epitrachys, respectively. While we fully respect their right not to accept our proposal, we cannot remain silent to their arguments that not only misinterpret our findings and statements but are often in direct conflict with their own results that actually support our proposal to segregate Lophiolepis. In addition, as Moreyra and co-authors did not include Epitrachys italica (formerly Cirsium italicum) in their analyses; they have no basis for arguing in favour or against our proposal to separate it as a monotypic genus. Finally, we conclude that the genus Cirsium, as circumscribed by the above-mentioned authors (i.e., including Lophiolepis), is definitively not monophyletic.

Background: Genome size is influenced by natural selection and genetic drift acting on variations from polyploidy and repetitive DNA sequences. We hypothesized that centromere drive, where centromeres compete for inclusion in the functional gamete during meiosis, may also affect genome and chromosome size. This competition occurs in asymmetric meiosis, where only one of the four meiotic products becomes a gamete. If centromere drive influences chromosome size evolution, it may also impact post-polyploid diploidization, where a polyploid genome is restructured to function more like a diploid through chromosomal rearrangements, including fusions. We tested if plant lineages with asymmetric meiosis exhibit faster chromosome size evolution compared to those with only symmetric meiosis, which lack centromere drive as all four meiotic products become gametes. We also examined if positive selection on centromeric histone H3 (CENH3), a protein that can suppress centromere drive, is more frequent in these asymmetric lineages. Methods: We analysed plant groups with different meiotic modes: asymmetric in gymnosperms and angiosperms, and symmetric in bryophytes, lycophytes and ferns. We selected species based on available CENH3 gene sequences and chromosome size data. Using Ornstein–Uhlenbeck evolutionary models and phylogenetic regressions, we assessed the rates of chromosome size evolution and the frequency of positive selection on CENH3 in these clades. Results: Our analyses showed that clades with asymmetric meiosis have a higher frequency of positive selection on CENH3 and increased rates of chromosome size evolution compared to symmetric clades. Conclusions: Our findings support the hypothesis that centromere drive accelerates chromosome and genome size evolution, potentially also influencing the process of post-polyploid diploidization. We propose a model which in a single framework helps explain the stability of chromosome size in symmetric lineages (bryophytes, lycophytes and ferns) and its variability in asymmetric lineages (gymnosperms and angiosperms), providing a foundation for future research in plant genome evolution.

Summary: Angiosperms with large genomes experience nuclear‐, cellular‐, and organism‐level constraints that may limit their phenotypic plasticity and ecological niche, which could increase their risk of extinction. Therefore, we test the hypotheses that large‐genomed species are more likely to be threatened with extinction than those with small genomes, and that the effect of genome size varies across three selected covariates: life form, endemism, and climatic zone. We collated genome size and extinction risk information for a representative sample of angiosperms comprising 3250 species, which we analyzed alongside life form, endemism, and climatic zone variables using a phylogenetic framework. Genome size is positively correlated with extinction risk, a pattern driven by a signal in herbaceous but not woody species, regardless of climate and endemism. The influence of genome size is stronger in endemic herbaceous species, but is relatively homogenous across different climates. Beyond its indirect link via endemism and climate, genome size is associated with extinction risk directly and significantly. Genome size may serve as a proxy for difficult‐to‐measure parameters associated with resilience and vulnerability in herbaceous angiosperms. Therefore, it merits further exploration as a useful biological attribute for understanding intrinsic extinction risk and augmenting plant conservation efforts.

Species of the carnivorous family Lentibulariaceae exhibit the smallest genomes in flowering plants. We explored the hypothesis that their minute genomes result from the unique mitochondrial cytochrome c oxidase (COX) mutation. The mutation may boost mitochondrial efficiency, which is especially useful for suction-bladder traps of Utricularia, but also increase DNA-damaging reactive oxygen species, leading to genome shrinkage through deletion-biased DNA repair. We aimed to explore the impact of this mutation on genome size, providing insights into genetic mutation roles in plant genome evolution under environmental pressures. We compiled and measured genome and mean chromosome sizes for 127 and 67 species, respectively, representing all three genera (Genlisea, Pinguicula and Utricularia) of Lentibulariaceae. We also isolated and analysed COX sequences to detect the mutation. Through phylogenetic regressions and Ornstein–Uhlenbeck models of trait evolution, we assessed the impact of the COX mutation on the genome and chromosome sizes across the family. Our findings reveal significant correlations between the COX mutation and smaller genome and chromosome sizes. Specifically, species carrying the ancestral COX sequence exhibited larger genomes and chromosomes than those with the novel mutation. This evidence supports the notion that the COX mutation contributes to genome downsizing, with statistical analyses confirming a directional evolution towards smaller genomes in species harbouring these mutations. Our study confirms that the COX mutation in Lentibulariaceae is associated with genome downsizing, probably driven by increased reactive oxygen species production and subsequent DNA damage requiring deletion-biased repair mechanisms. While boosting mitochondrial energy output, this genetic mutation compromises genome integrity and may potentially affect recombination rates, illustrating a complex trade-off between evolutionary advantages and disadvantages. Our results highlight the intricate processes by which genetic mutations and environmental pressures shape genome size evolution in carnivorous plants.

The invasive tetraploid Cirsium vulgare hybridizes with both Cirsium and Lophiolepis. Its conflicted position in molecular phylogenies, and its peculiar combination of morphological, anatomical, and genomic features that are alternatively shared with representatives of Cirsium or Lophiolepis, strongly suggest its intergeneric hybrid origin. Genetic relationships of C. vulgare (8 samples) with genus Lophiolepis (11 species) and other representatives of genus Cirsium (12 species) were evaluated using restriction site‐associated DNA sequencing (RADseq) and examined using analytical and imaging approaches, such as NeighborNet, Heatmap, and STRUCTURE, to identify nuclear genomes admixture. Estimation of the intensity of spontaneous hybridization within and between Cirsium and Lophiolepis was based on herbarium revisions and published data for all reported hybrids pertinent to taxa currently included in Cirsium or Lophiolepis. The genome of any examined Cirsium species is more similar to C. vulgare than to any Lophiolepis species, and vice versa. The nuclear genome of the tetraploid C. vulgare is composed of two equivalent parts, each attributable either to Lophiolepis or to Cirsium; the organellar RADseq data clustered C. vulgare with the genus Cirsium. Spontaneous hybridization between Cirsium and Lophiolepis is significantly less intensive than within these genera. Our analyses provide compelling evidence that the invasive species C. vulgare has an allotetraploid intergeneric origin, with the maternal parent from Cirsium and the paternal from Lophiolepis. For the purpose of delimiting monophyletic genera, we propose keeping Lophiolepis separate from Cirsium and segregating C. vulgare into the hybridogenous genus Ascalea.