Integrated metabolomics and transcriptomics reveal mechanisms underlying high-yield accumulation of 10-deacetylbaccatin III, baccatin III, and 10-deacetyltaxol in Taxus mairei twigs

Taxus renewable twigs produce valuable taxanes, notably anticancer drug paclitaxel and its key intermediates, including 10-deacetylbaccatin III (10DAB), baccatin III (B-III), and 10-deacetyltaxol (10DAT). However, incomplete understanding of taxane biosynthetic networks and their regulatory mechanisms across species and developmental stages limits targeted genetic improvement of these medicinal plants. Here, we integrated metabolomics and transcriptomics to analyze taxane accumulation and associated biosynthetic gene expression patterns in three high-yielding (10DAB- or paclitaxel-rich) Taxus accessions (HZDNF, HZDDB, HZDMDY) twigs across developmental stages grown under uniform environmental conditions. Our study identified 55 distinct taxanes and 140 differentially expressed genes (DEGs) related to paclitaxel biosynthesis, enabling construction of relatively comprehensive metabolic networks and gene co-expression patterns. The HZDNF variety, particularly its young twigs (NF-new), showed exceptional production of most 6/8/6/4-taxanes (including 10DAB, B-III, and 10DAT), outperforming other varieties. This correlated with elevated expression of 42 potentially biosynthetic genes, including 10 putative rate-limiting enzyme genes. Furthermore, weighted gene co-expression network analysis (WGCNA) revealed 34 core DEGs from the above-mentioned 42 candidates, along with 13 potential master transcriptional factors (TFs). These TFs might enhance core DEGs expression via direct or indirect means, thereby boosting 10DAB/B-III/10DAT accumulation and high yield. Subsequent functional verification for two representative TFs of 13 candidates through transient overexpression, confirmed that two novel TFs (bHLH-16 and zf-HD-6) significantly enhance 10DAB/10DAT production by activating key DEGs ( T7βOH-1 , T10βOH-2 and BAPT-2 ). These findings advance understanding of taxane biosynthesis (especially 10DAB, B-III and 10DAT), providing targets for metabolic engineering of taxanes and Taxus germplasm improvement. • HZDNF twigs (especially NF-new) showed high-accumulation of 10DAB/B-III/10DAT. • HZDNF twigs (especially NF-new) showed metabolic specialization to 6/8/6/4-taxanes. • 34 core DEGs showed vital positive correlations with 10DAB/B-III/10DAT production. • 13 potential master TFs upregulate core DEGs to boost 10DAB/B-III/10DAT production. • bHLH-16/zf-HD-6 chosen from 13 TFs were validated to boost 10DAB/10DAT production.