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

BACKGROUND: Invasive plants pose a major threat to global biodiversity, yet the molecular and genomic mechanisms underlying their success remain poorly understood. Here, we investigate the invasion of the common reed Phragmites australis, a grass species that became invasive in North America after its introduction from Europe, to elucidate the molecular mechanisms potentially underlying its invasion process. RESULTS: By integrating single-cell RNA sequencing, spatial transcriptomics, and comparative genomics, we construct a single-cell atlas of Phragmites australis, and identify 19 transcriptionally distinct cell types, including meristematic cells, parenchyma, mesophyll, epidermal, and vascular tissues. Comparative analysis of common garden-grown native populations from Europe and invasive populations from North America reveals a significant proportion of differentially expressed genes located on B chromosomes, which show copy number expansion in invasive genomes. Four B-chromosome genes, PaChr24B.43 (IMP-α3), PaChr24B.82 (GATA2), PaChr24B.218 (SCC3), and PaChr24B.240 (SCC3), are consistently differentially expressed between invasive and noninvasive populations across nearly all cell types. At the tissue level, mesophyll, parenchyma, vascular, and epidermal cells in the invasive population all exhibit increased gene expression in response to sugar starvation and light deprivation. Epidermal cells also show strong activated gene expression in response to hypoxia but suppressed expression of genes involved in the defence related respiratory burst. CONCLUSIONS: This study establishes a cell type-resolved molecular atlas of a nonmodel invasive plant and reveals cell type-specific gene regulatory mechanisms within the regenerative shoot system. These findings advance our understanding of the cellular and genomic basis of plant invasiveness and provide a foundation for future ecological research and management.