Biology subjects

Cordier, J.

Publications and source records attributed to Cordier, J..

2 recordsLinked to original sources

bioRxiv2026

Range wide analysis of genetic diversity and structure gives insights into Rosa gallica L. evolutionary history

Rosa gallica L., the French rose, is a perennial, tetraploid, heterozygous species that naturally propagates by seed and sucker. It occurs in the wild, primarily in Europe, and also exists as cultivated varieties. R. gallica cultivars were extensively bred and cultivated in France at the beginning of the 19th century. Although several hypotheses have been proposed regarding the species expansion based on historical records, none have been assessed using molecular data. Indeed, its genetic diversity has so far been investigated only at local or regional scales, hindering the identification of the evolutionary factors shaping its present-day distribution. Using 29 sequenced microsatellites, we genotyped a comprehensive sample of 1618 individuals, including wild R. gallica from 219 sites across the species range, rose cultivars, and specimens from other Rosa species. We then detected clonal lineages and characterized the range-wide genetic diversity and structure, aiming to disentangle the roles of natural and human factors in shaping the distribution of R. gallica, with particular focus on France. French diversity appears particularly structured compared to the rest of the range, suggesting multiple origins within France. Populations in South Alps, Central Eastern Europe, and Eastern France appear to have recolonized naturally from a single southern glacial refugium. In contrast, populations in the western part of France likely resulted from more recent natural or human-mediated dispersal. Finally, clonal lineages containing both wild and cultivated individuals were predominantly found in France, highlighting the role of human-mediated dispersal in 28 of the 98 French sites studied. These findings show that the present-day natural range of R. gallica was shaped primarily by post-glacial recolonization, but also reveal a contribution of human activities to its recent dispersal, particularly in France, where cultivated varieties were intensively bred and exchanged.

genetics↗

bioRxiv2025

Extending cis-regulatory networks using chromatin-RNA interactions

Cis-regulatory networks are essential for determining gene transcriptional states, yet the mechanisms that mediate cellular signaling and enhancer-promoter communications are not yet well understood. Here, we integrate high-resolution enhancer-promoter interactions obtained using targeted chromosome conformation capture and RNA-DNA contacts from RADICL-seq to uncover the role of RNA in modulating enhancer-promoter interactions. Both datasets were generated from human induced pluripotent cells at different stages across neural differentiation. As expected, most enhancer-promoter interactions were dynamic with only 38% shared across all cell states and 68% of promoter interacting regions overlapped at least one annotated neural enhancer. Integration with RADICL-seq data revealed a 9.3-fold enrichment for cis-interacting DNA regions to associate with at least one RNA. Among 18,346 cis-interacting promoters, only 1,170 (6.3%) lacked any RNA association, whereas 3,702 (28%) showed stable RNA association and 13,579 (74%) displayed dynamic RNA association across differentiation. Promoters associated with RNA engaged with higher number of enhancers and exhibited higher expression levels, while enhancers with RNA associations showed higher levels of chromatin activation marks. Promoters with dynamic RNA association were also more likely to be differentially expressed and enriched for relevant biological processes, phenotypes and diseases. Importantly, RNA-DNA association dynamics correlated strongly with DNA-DNA interaction dynamics; gain of RNA association on enhancers was typically accompanied by enhancer-promoter interaction gain, whereas concurrent RNA association gain on both promoter and enhancers frequently led to interaction loss. The correlation of RNA association on cis-interaction dynamics across differentiation were also captured in the community structure of the DNA-RNA network. Together, our results reveal extensive coupling between RNA-DNA and DNA-DNA networks supporting a coordinating role of RNA in gene regulation.

genomics↗