Integrated Transcriptomic and Metabolomic Analysis Reveals Biochar-Induced Enhancement of Growth and Secondary Metabolism in the Medicinal Plant Echinacea purpurea

<i>Echinacea purpurea</i> (L.) Moench is a medicinally valuable plant with well-documented pharmacological properties; however, its physiological and molecular responses to biochar amendment remain largely unexplored. This study applied integrated transcriptomic and metabolomic approaches to investigate the underlying mechanisms of biochar-induced effects in <i>E. purpurea</i>. Biochar amendment significantly promoted plant growth and improved nutrient status. Concurrent transcriptomic analysis revealed the molecular basis for these changes, identifying 4733 differentially expressed genes (DEGs). Further analysis showed significant enrichment in plant hormone signal transduction pathways, particularly those of auxin and jasmonic acid (JA). The activation of the JA pathway was specifically validated by the concurrent upregulation of its biosynthetic and metabolic genes, together with the marked accumulation of JA, jasmonoyl-isoleucine, and 12-hydroxy-jasmonoyl-isoleucine. Metabolomic profiling further revealed a pronounced upregulation of phenylpropanoid pathway metabolites, including 3-hydroxy-4-methoxycinnamic acid, chlorogenic acid methyl ester, ferulic acid O-hexoside, and coumarin derivatives such as 7-methoxy-4-methylcoumarin. Correlation analysis of transcriptomic and metabolomic data confirmed the concurrent up-regulation of phenylpropanoid biosynthetic genes. These integrated results reveal the mechanistic basis through which biochar application simultaneously promotes growth and enhances the secondary metabolism of <i>E. purpurea</i> by coordinately activating phytohormone signaling and phenylpropanoid biosynthesis. These results establish the potential of biochar in enhancing <i>E. purpurea</i> cultivation, with future work needed to determine optimal application rates.