Elucidating the wedelolactone biosynthesis pathway from Eclipta prostrata (L.) L.: a comprehensive analysis integrating de novo comparative transcriptomics, metabolomics, and molecular docking of targeted proteins.

Eclipta prostrata belongs to the Asteraceae family. The plant contains bioactive compounds like wedelolactone (WDL) and demethylwedelolactone (DW). Its transcriptomic information engaged with secondary metabolite biosynthesis is not available. Based on differential accumulation of WDL and DW in root, shoot of the mature plant, we performed comparative de novo transcriptome of root and shoot tissue in three independent biological replicates and generated 49820 unique transcripts. Annotation resulted in significant matches for 43,015 unigenes. Based on differential gene expression data, we found WDL biosynthesis-related transcripts, which were mainly upregulated in shoot. Finally, 13 selected differentially expressed transcripts related to WDL biosynthesis that were validated by qRT-PCR. Detailed tissue-specific metabolite and transcript profiling revealed that DW highly accumulated in root and WDL accumulation was high in aerial part along with transcripts. For WDL pathway exploration, we did integrated profiling of 08 metabolites and 13 transcripts and witnessed that only naringenin, apigenin, DW, and WDL were detected in different developmental stages. Taking leads from the findings, we postulated that naringenin to apigenin pathway is one potential route for WDL biosynthesis. Moreover, wound stress led to accumulation of DW and WDL and related biosynthetic transcripts. Furthermore, the selected enzymes were subjected to molecular docking and binding studies for the predicted substrates involved in crucial and advance steps of WDL biosynthesis. A comprehensive analysis integrating de novo transcriptomics, metabolomics, and molecular docking of targeted proteins paves the way for the elucidation of the putative wedelolactone biosynthesis pathway from E. prostrata.