Single-nucleus transcriptomic profiling reveals cell type-specific gene expression and regulatory networks in Camellia sinensis root tips

The root system serves as the primary organ for water and nutrient absorption in plants, with its architecture significantly influencing the growth efficiency and environmental adaptability of tea plant. While present knowledge of the cellular and molecular mechanisms underlying root growth largely derives from studies on the dicot model Arabidopsis. To enrich the research on the development of tea plant root cell types, this study expanded the snRNA-seq scope to tea plant by presenting transcriptomic data from 37,922 single cells at the root tips, identifying 18 transcriptionally distinct clusters and 8 major cell types. Our analysis elucidated specific regulatory programs associated with each cell type, encompassing biosynthesis, signaling, and response to secondary metabolites and phytohormone. The comparison of major cell types between tea plant and Arabidopsis reveals a degree of functional conservation in the meristem, stele, and lateral root cap. Significant differences were observed in pathways related to "biological process," "protein binding," and "defense response". Through the integration of gene expression analysis in tea plant cell types with the identification and bioinformatics analysis of AUX1/LAX gene family, the CSS0011345 gene was identified and designated as CsLAX1. It was specifically expressed in the lateral root cap, and transgenic verification shown that CsLAX1 could affect root system architecture by regulating the number of lateral roots and the length of primary roots. In general, we enriched the single-nucleus transcriptome data of woody plant roots and provided worthwhile resources for studying the identification, physiological function and evolutionary analysis of different cell types in tea plant. These results lay a foundation for understanding woody plant biology at the single-nucleus level.