Single-cell ATAC sequencing illuminates the cis-regulatory differentiation of taxol biosynthesis between leaf mesophyll and leaf epidermal cells in Taxus mairei

Taxol is a widely used anticancer drug; however, its accumulation pattern can vary largely among leaf tissues. Taxol biosynthesis is driven by a series of transcription factors (TFs), but the extent of chromatin changes that functionally regulate gene expression associated with taxol biosynthesis remain poorly understood. To assess the effects of tissue heterogeneity on taxol biosynthesis, we applied single-cell transposase-accessible chromatin sequencing to Taxus mairei leaves and identified differentially accessible regions. We captured 9488 independent cells with 42,192 fragment reads per cell. In total, 66.64% were confidently mapped onto the T. mairei genome. Projection analysis divided all the cells into nine clusters, which suggests a high degree of cell heterogeneity in T. mairei leaves. Based on the cell type markers, Clusters 2 and 7 were annotated as leaf mesophyll cells, and Clusters 5 and 6 were annotated as leaf epidermal cells. A differential accessibility analysis identified 9600 and 8538 leaf mesophyll and epidermal, respectively, cell-specific open chromatin regions. We predicted the genomic features of the genes involved in different stages of taxol biosynthesis, and there was a close correlation between chromatin open peaks and the expression levels of several taxol biosynthesis-related genes. We further identified a number of cell type-specific TF motifs and reference TFs that appeared to be involved in taxol biosynthesis. The study of T. mairei leaves at a single-cell resolution provides a valuable resource for determining the basic principles of the cell type-specific regulation of taxol biosynthesis.