Single-cell RNA-sequencing profiles reveal the developmental landscape of hawthorn leaves.

Its leaves accumulate valuable secondary metabolites, including flavonoids, and have long been used in traditional Chinese medicine. Despite available chromosome-level genome assemblies and bulk transcriptome data, the cellular composition of hawthorn leaves, their developmental trajectories, and the cell-type-specific distribution of biosynthetic gene expression remain uncharacterized.

Here we report the first single-cell transcriptomic atlas of hawthorn leaves, generated by integrating protoplast-based scRNA-seq and nucleus-based snRNA-seq from two species (C. pinnatifida var. major N. E. Br. and C. scabrifolia (Franch.) Rehder). From four libraries, we profiled 32,292 high-quality cells, resolved sixteen transcriptional clusters, and annotated nine canonical cell types: mesophyll, pavement, guard, xylem, metaxylem, phloem parenchyma, companion, sieve element, and meristematic cells.