A multi-tissue single-cell atlas of moso bamboo ( Phyllostachys edulis ) reveals cellular heterogeneity and lineage trajectories

Abstract

Moso bamboo (Phyllostachys edulis) is a high-value renewable resource used for timber, fiber, and carbon sequestration, yet the cellular basis of its development remains poorly resolved. Here, we performed a systematic single-cell RNA-sequencing (scRNA-seq) analysis of moso bamboo seedlings, generating 31,658 high-quality single-cell transcriptomes. Initial unsupervised graph-based clustering partitioned the dataset into 23 clusters, which were subsequently assigned to 11 major cell-type categories through marker-guided and biologically informed annotation, including meristemoid, coleoptile L1 epidermis, cortex, epidermis, mesophyll precursor, mestome sheath, pericycle, phloem, endodermis, root cap, and xylem. Pseudo-time analysis suggested putative vascular-associated trajectories in which captured xylem and phloem cells were ordered along a bifurcating structure extending from meristem populations. Xylem cells were enriched in cell wall modification genes, while phloem cells preferentially expressed transport- and defense-related genes. Root cell differentiation exhibited polar patterning, progressing through seven stages from meristems to epidermis, endodermis, cortex, and root cap lineages. Leaf development followed a unidirectional trajectory from meristems to mestome sheath cells and coleoptile L1 epidermis, and ultimately to mesophyll cells. We further identified key regulatory factors underlying these cellular differentiations, revealing developmental path differences among roots, stems, and leaves. This study constructs a high-resolution cellular atlas of moso bamboo seedlings that delineates developmental programs underlying rapid growth and environmental adaptation, and uncovers dynamic trajectories from meristems to specialized cell types. These findings provide candidate regulators for future genetic studies to enhance biomass production and stress tolerance in moso bamboo.