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

作者：Guigang Zhao, Xien Wu, Baozheng Wang, Xiaolu Li, Junjuan Zheng, Zhaoli Ding, guodong Li, Ticao Zhang · 发表于：BMC Plant Biology · 年份：2026 · DOI：10.1186/s12870-026-09127-z · 研究领域：Botanical Studies and Applications、Plant Molecular Biology Research、Plant Gene Expression Analysis

Hawthorn (Crataegus spp.) is an economically and medicinally important genus in Rosaceae. 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. Cell-type-resolved interspecific comparison identified 642 differentially expressed genes between species, with divergent enrichment of photosynthesis and volatile biosynthesis processes in C. pinnatifida var. major and hypoxia-response processes in C. scabrifolia. Pseudotime analysis reconstructed branched developmental trajectories converging on mesophyll dominance at late stages, consistent with classical dicotyledonous leaf organogenesis. Cell-type-resolved profiling demonstrated spatial partitioning o...