Advances in omics technologies now permit the generation of highly contiguous genome assemblies, detection of transcripts and metabolites at the level of single cells and high-resolution determination of gene regulatory features. Here, using a complementary, multi-omics approach, we interrogated the monoterpene indole alkaloid (MIA) biosynthetic pathway in Catharanthus roseus, a source of leading anticancer drugs. We identified clusters of genes involved in MIA biosynthesis on the eight C. roseus chromosomes and extensive gene duplication of MIA pathway genes. Clustering was not limited to the linear genome, and through chromatin interaction data, MIA pathway genes were present within the same topologically associated domain, permitting the identification of a secologanin transporter. Single-cell RNA-sequencing revealed sequential cell-type-specific partitioning of the leaf MIA biosynthetic pathway that, when coupled with a single-cell metabolomics approach, permitted the identification of a reductase that yields the bis-indole alkaloid anhydrovinblastine. We also revealed cell-type-specific expression in the root MIA pathway.

组学技术的进步现在允许生成高度连续的基因组组装、在单细胞水平上检测转录物和代谢物以及高分辨率地确定基因调控特征。在这里，我们使用互补的多组学方法，研究了长春花（主要抗癌药物的来源）中的单萜吲哚生物碱（MIA）生物合成途径。我们在八个C.roseus染色体上鉴定了参与 MIA 生物合成的基因簇和 MIA 途径基因的广泛基因重复。聚类不限于线性基因组，通过染色质相互作用数据，MIA 途径基因存在于相同的拓扑相关域内，从而可以识别 secologanin 转运蛋白。单细胞 RNA 测序揭示了叶 MIA 生物合成途径的连续细胞类型特异性划分，当与单细胞代谢组学方法相结合时，可以鉴定产生双吲哚生物碱脱水长春花碱的还原酶。我们还揭示了根 MIA 通路中的细胞类型特异性表达。