Biology subjects

Bures, P.

Publications and source records attributed to Bures, P..

4 recordsLinked to original sources

bioRxiv2026

Nowhere to Hide: The Effect of Centromere Architecture on LTR Retrotransposon Dynamics

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.

evolutionary biology↗

bioRxiv2025

Chromosome Size as a Universal Predictor of Recombination Rate: Insights from Holocentric and Monocentric Systems

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 summaryWhy 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.

genetics↗

bioRxiv2023

Genome size is positively correlated with extinction risk in herbaceous angiosperms

O_LIAngiosperms with large genomes experience nuclear-, cellular- and organism-level constraints that may limit their phenotypic plasticity and ecological niche. These constraints have been documented to vary across lineages, life-history strategies, ecogeographic patterns and environmental conditions. Therefore, we test the hypotheses that extinction risk is higher in large-genomed compared to small-genomed species, and that the effect of genome size varies across three selected covariates: life form, endemism, and climatic zones. C_LIO_LIWe collated genome size and extinction risk information for a representative sample of angiosperms comprising 3,250 species, which we analyzed alongside life form, endemism and climate variables using a phylogenetic framework. C_LIO_LIAngiosperm 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 also influences extinction risk directly and significantly. C_LIO_LIGenome 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. C_LI

plant biology↗

bioRxiv2022

The global biogeography of angiosperm genome size is shaped by climate and range size

O_LIAngiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large-genome-constraint, mutational-hazard, polyploidy-mediated, and climate-mediated hypotheses. C_LIO_LIWe compiled the largest genome size dataset to date, encompassing >5% of known angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. C_LIO_LIWe observed that angiosperms with large range sizes generally had small genomes, supporting the large-genome-constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50{degrees}N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40-50{degrees}N northwards. C_LIO_LIOur analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically-mediated purifying selection, genetic drift, relaxed selection, and environmental filtering. C_LI

evolutionary biology↗