The plant ontology of cell types

The advent of single-cell genomic technologies has revolutionized plant cell biology by revealing cellular heterogeneity in plant tissues and organs with unprecedented resolution. Methods like single-cell transcriptomics, epigenomics, and multi-omics integration have deepend insights into molecular mechanisms governing plant development, function, and evolutionary adaptations (Xu and Jackson, 2025). Notably, these approaches have facilitated comprehensive cell atlases mapping gene expression, chromatin accessibility, and regulatory networks across species (Wang et al., 2025; Guo et al., 2025), identifying marker genes, differentiation trajectories, and spatiotemporal regulatory in processes like root development, and seed germination (Zhang et al., 2021; Yao et al., 2024). However, proliferating single-cell studies face a major bottleneck from inconsistent cell type annotations, which impede data integration and crossspecies comparison. A unified, phylogenetically informed atlas of plant cellular diversity is essential for elucidating molecular developmental and evolutionary principles (Sebé-Pedrós et al., 2025).