Cell type specific regulation of phenolic acid and flavonoid metabolism in Taxus mairei leaves

Abstract

The Taxus tree is an important industrial resource for the extraction of Taxol, a natural anticancer drug. Recently, numerous active compounds, such as phenolic acids and flavonoids, were identified in the leaves of Taxus mairei. However, the distribution and biosynthesis of phenolic acids and flavonoids in Taxus leaves are largely unknown. Integrated MALDI-IMS, ScRNA-seq and ScATAC-seq analysis was used to reveal the cell type-specific regulation of phenolic acid and flavonoid biosynthesis. Based on the cluster-specifically expressed genes, ScRNA-seq grouped the cells into 12 clusters, while ScATAC-seq grouped the cells into 9 clusters, indicating a high degree of leaf cell heterogeneity. Several marker genes were selected for cell type annotation, some of which were effectively verified by in situ hybridization. ScRNA-seq identified four phenolic acid and flavonoid biosynthesis-related genes (each one > 5 % cell coverage), which significantly expressed in the leaf epidermal cells. The cell-specific open chromatin regions surrounding the four phenolic acid and flavonoid biosynthesis-related genes were enriched in the epidermal cells. We further identified several cell type-specifically expressed transcription factors that might be involved in the biosynthesis of phenolic acids and flavonoids. Our study provided valuable information for studying the cell type specific regulation of phenolic acid and flavonoid biosynthesis in Taxus leaves.