Single-cell transcriptome atlas reveals spatiotemporal developmental trajectories in the basal roots of Moso bamboo (<i>Phyllostachys edulis</i>)

Abstract Roots are essential for plant growth and development. Bamboo is a large Poaceae perennial with 1,642 species worldwide. However, little known about the transcriptional atlas that underpin root cell-type differentiation. Here, we set up modified protocol protoplast preparation reported single-cell transcriptomes of 14,279 filtered single cells derived from basal tips Moso bamboo. We identified four cell types defined new type-specific marker genes root. reconstructed developmental trajectories cap, epidermis, ground tissues elucidated critical factors regulating fate determination. According to in situ hybridization pseudotime trajectory analysis, cap epidermis originated common initial lineage, revealing particularity bamboo further key regulatory these differentiation indicated divergent pathways between rice. Additionally, PheWOX13a PheWOX13b ectopically expressed Arabidopsis inhibited primary lateral regulated development which was different WOX13 orthologs Arabidopsis. Taken together, our results offer an important resource investigating mechanism system architecture woody Bambusoideae.