Bailes, E. J. | 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↗

bioRxiv2026

Horizontal gene transfer fuels metabolic innovation in the grass Zuloagaea bulbosa

Horizontal gene transfer (HGT) allows the movement of DNA across broad evolutionary distances without sexual reproduction. In grasses, HGT is widespread and although a few horizontally transferred genes (HTG) are adaptive, most are purged over time. Within the adaptive HTG, biosynthetic genes encoding enzymes that act together in the same pathway and physically co-localise in clusters have been reported multiple times. The aims of this study are to test whether HGT is bidirectional in a pair of grass species, maize and Zuloagaea bulbosa, and if HTGs are found more than expected by chance in biosynthetic genes organised in clusters. To achieve this, we firstly generated a phased reference genome for Z. bulbosa. Then we identified 56 candidate horizontally transferred genes, of which 45% were from Andropogoneae, including two likely to be of maize origin. Since transfers from Z. bulbosa to maize were previously described, our results show that HGT is bidirectional, although the balance might not be even. After predicting all biosynthetic gene clusters in the Z. bulbosa genome, we found that HTGs are enriched in biosynthetic genes organised in clusters. This correlation between HGT and gene clustering is likely to be a consequence of selection due to the immediate adaptive benefit a whole pathway can provide. Two of the HTGs from Andropogoneae belong to the benzoxazinoid BGC, which previously underwent an ancestral transfer from Panicoideae into Pooideae. The dynamism of biosynthetic gene clusters, including recurrent horizontal gene transfers, contributes to the extraordinary metabolic diversity present in plants. Significance statementHorizontal gene transfer (HGT) is a significant driver of evolution that is widespread in grasses. In this study, we show for the first time reciprocal transfer of DNA between maize and another Mexican grass, Zuloagaea bulbosa. This result represents a proof of concept of bidirectional HGT which allows for limited, recurrent gene flow among distant species. Furthermore, we show that horizontally transferred genes are enriched for biosynthetic genes organised in biosynthetic gene clusters, regions of the genome that encode for multiple enzymes that act in the same biosynthetic pathway. We hypothesise that the transfer of a complete multi-genic pathway, ready to be used and potentially offering an evolutionary advantage, might promote a predominant retention of gene clusters in comparison with background HGT.

genomics↗