Methyl jasmonate treatment reveals novel insights into lncRNA-mediated regulation of secondary metabolite biosynthesis pathways in Echinacea purpurea

RNA-seq analysis has revolutionized the discovery of long non-coding RNAs (lncRNAs) in medicinal plants like Echinacea purpurea(L.) Moench, commonly known as purple coneflower. These lncRNAs potentially play crucial roles in regulating the biosynthesis of bioactive secondary metabolites. Our study aimed to identify regulatory lncRNAs involved in these pathways by treating 40-day-old E. purpureaseedlings with 100 μM methyl jasmonate (MeJA). Subsequently, RNA-sequencing was performed, identifying 509 differentially expressed transcripts for co-expression network analysis. The correlation between differentially expressed lncRNAs and coding transcripts was calculated, constructing a gene network to identify hub lncRNAs and their associated genes. Gene ontology and KEGG enrichment analyses were conducted to gain insights into the functions of these hub differentially expressed lncRNAs (DElncRNAs). Results revealed that these hub DElncRNAs regulate key genes involved in various pathways. For instance, CSE and BEBT are associated with the conversion of caffeoylshikimate to caffeate and shikimate, respectively. Additionally, SAT and NEC3 contribute to alkaloid biosynthesis, while NES1 and CFAT are involved in the biosynthesis of aromatic compounds, phenylpropanoids, and terpenoids. HST and SILD are associated with lignin biosynthesis. Furthermore, these lncRNAs mediate the acyl group transfer on both shikimate and quinate in the phenylpropanoid and flavonoid biosynthesis pathways. In summary, our findings offer comprehensive insights into the transcriptomic and metabolomic changes induced by methyl jasmonate treatment. We provide novel insights into the regulatory mechanisms of secondary metabolite biosynthesis, specifically highlighting the role of lncRNAs in E. purpurea.