Integrated mass spectrometry imaging and single‐cell transcriptome atlas strategies provide novel insights into taxoid biosynthesis and transport in Taxus mairei stems

SUMMARY Taxol, which is a widely used important chemotherapeutic agent, was originally isolated from Taxus stem barks. However, little is known about the precise distribution of taxoids and the transcriptional regulation of taxoid biosynthesis across Taxus stems. Here, we used MALDI‐IMS analysis to visualize the taxoid distribution across Taxus mairei stems and single‐cell RNA sequencing to generate expression profiles. A single‐cell T. mairei stem atlas was created, providing a spatial distribution pattern of Taxus stem cells. Cells were reordered using a main developmental pseudotime trajectory which provided temporal distribution patterns in Taxus stem cells. Most known taxol biosynthesis‐related genes were primarily expressed in epidermal, endodermal, and xylem parenchyma cells, which caused an uneven taxoid distribution across T. mairei stems. We developed a single‐cell strategy to screen novel transcription factors (TFs) involved in taxol biosynthesis regulation. Several TF genes, such as endodermal cell‐specific MYB47 and xylem parenchyma cell‐specific NAC2 and bHLH68, were implicated as potential regulators of taxol biosynthesis. Furthermore, an ATP‐binding cassette family transporter gene, ABCG2, was proposed as a potential taxoid transporter candidate. In summary, we generated a single‐cell Taxus stem metabolic atlas and identified molecular mechanisms underpinning the cell‐specific transcriptional regulation of the taxol biosynthesis pathway. Significance Statement Integrating mass spectrometry imaging and single‐cell transcriptome atlas strategies, we created a single‐cell T. mairei stem atlas and provided a spatial distribution pattern of Taxus stem cells. Screening for novel transcription factors helped us to reveal the molecular mechanisms underpinning the cell‐specific transcriptional regulation of the taxol biosynthesis pathway.