Hibdige, S. G. | Search bioRxiv

bioRxiv2026

Genomic signatures of local adaptation in marram grass highlight the importance of provenance in dune restoration

Coastal sand dunes provide critical natural flood defences and key habitats for a range of threatened species. These systems are formed when shifting sands are stabilised by specialised coastal grasses. In Europe, marram grass (Calamagrostis arenaria) is the main dune building species. However, despite its ecological importance and its widespread use in dune restoration, little is known about the genomic innovations that facilitated the colonisation of the coast, the extent of local adaptation in current populations, or the genetic consequences of restoration practices. Using a chromosome-scale reference genome we generate here, we show that C. arenaria has significant expansions in several gene families relevant to coastal adaptation, including those associated with salinity, drought, and nutrient limitation. Using ddRAD-Seq data for over 200 individuals from 10 European populations, we identified strong genetic differentiation between northern and southern populations which corresponds to recognised subspecies. Within the northern european populations, the genetic structure is largely driven by isolation-by-distance. Although, we detected evidence of non-local planting in a restored Swedish dune system, where introduced plants were genetically distinct from the native population and both groups exhibited reduced genetic diversity. Genome-wide scans for local adaptation within the northern European marram grass individuals identified outlying genomic regions that were enriched for genes with functions associated with nutrient deficiency, drought, pathogen defence, and other environmental stressors characteristic of coastal dunes, potentially indicating local adaptation. Outlying regions also include genes associated with lignin biosynthesis and culm mechanical strength, potentially reflecting selection on the structural properties required to withstand different burial and wind exposure regimes. Overall, these findings show widespread local adaptation in C. arenaria, and support the use of local provenance in dune restoration and conservation.

evolutionary biology↗

bioRxiv2025

Regulatory features determine the evolutionary fate of laterally acquired genes in plants

Lateral gene transfer (LGT) is widespread in eukaryotes, including in animals and plants where it can fuel adaptive evolution and innovation. However, the factors that influence the integration and long-term retention of transferred genes remain poorly understood. The pangenome of the grass Alloteropsis has a high turnover of laterally acquired genes, and here we combine expression, methylation and genomic data to identify factors promoting their long-term persistence. Most transferred genes appear to be degenerating, showing lower expression levels and/or greater sequence truncation compared to their vertically inherited homologs. These degenerating genes also show significantly higher levels of DNA methylation, potentially indicating transcriptional silencing. The likelihood of a transferred gene being retained will be influenced by how easily it can be expressed in the recipient genome. In Alloteropsis, putatively functional laterally acquired genes had expression levels significantly more similar to their donor xenolog than to their vertically inherited homolog. This pattern suggests that transferred genes may carry cis-regulatory elements encoded on the fragment of DNA that moves between species, facilitating their expression in the new genomic context. Evolutionary novelty may also increase the likelihood that selection retains a transferred gene. However, only a significant difference in expression level, not sequence divergence, between donor and recipient orthologs is associated with successful lateral gene transfer. Overall, our results show that most transferred genes degrade over time. However, those capable of regulating their own expression are more likely to persist and contribute to long-term evolutionary innovation. Significance StatementLateral gene transfer (LGT) can introduce novel traits into plant genomes, yet most transferred genes are only transient residents and are degenerating, with reduced expression, truncation, and elevated DNA methylation. However, a minority persist and are more likely to resemble their donor counterparts in expression, suggesting co-transfer of cis-regulatory elements. These findings indicate that regulatory compatibility is key to their long-term survival.

evolutionary biology↗