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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↗

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↗