Combined metabolomic and transcriptomic analysis reveals the characteristics of the lignan in Isatis indigotica Fortune

•Analyzed the synthase genes and compounds related to the lignan in diploid Isatis indigotica Fortune, tetraploid I.indigotica, and Isatis tinctoria Linnaeus through metabolomic and transcriptomic.•The analysis of transcription factors showed that the AP2-EREBP family (Iin24319), MYB family (Iin24843), and WRKY family (Iin08158) displayed expression patterns similar to Iin14549.•Serve as a reference for improving the quality of I. indigotica and developing germplasms with high lignan content. Lay a foundation for the functional characterization of UGTs in lignan biosynthesis pathway.