Single-cell and spatial transcriptomics in Phragmites australis reveal the association of B chromosomes with plant invasiveness

This study investigates the genetic basis of invasiveness in the common reed (Phragmites australis), a resilient grass species that became invasive in North America following its introduction from Europe. By integrating whole-genome sequencing with bulk, single-cell, and spatial transcriptomics, we constructed a comprehensive single-cell atlas of the common reed's shoot system.

UMAP analysis revealed 19 distinct cell clusters within the shoot, which were annotated using Gene Ontology (GO) enrichment to identify key cell types, including mesophyll, epidermal, bundle sheath, differentiating vascular cells, shoot apical meristems, and a cell cycle-associated cluster. We inferred key genes involved in the specification of several tissues, such as epidermal cells and ground meristems. For gene expression analysis, shoot tissues from three individuals of the invasive North American population and three from the native European population were included.