Transcriptomic and metabolomic analysis of allelopathic responses in Elymus nutans

To explore the allelopathic response mechanism of Elymus nutans to the extracts of Ligularia sagitta, seed germination tests combined with integrated transcriptome and metabolome analyses were performed to systematically investigate the effects of the extracts at different concentrations on its germination characteristics and molecular metabolism. The results showed that the concentration range of 0.01-0.10 mg/mL was the sensitive interval for the allelopathic response of Elymus nutans to the extracts of Ligularia sagitta, and germination energy (GE) exhibited higher sensitivity to allelopathic stress than germination rate (GR). Transcriptome analysis yielded a total of 367463 Unigenes. In the comparison group of A and B,5617 differentially expressed genes (DEGs) were identified, including 3122 down-regulated genes and 2495 up-regulated genes. GO enrichment analysis revealed that these DEGs were mainly involved in biological processes such as biosynthesis and structural constituents of ribosomes. KEGG analysis indicated that 2683 DEGs were mapped to 133 pathways, of which 14 were significantly enriched, mainly covering pathways related to secondary metabolite biosynthesis, ribosome, and plant hormone signal transduction. Metabolome analysis identified 361 differential metabolites (DMs), which were annotated to 79 pathways with 29 significantly enriched ones. Integrated transcriptome and metabolome analysis revealed that DEMs and DMs were mainly enriched in two KEGG functional categories, namely Genetic Information Processing and Metabolism. Among these, the phenylpropanoid biosynthesis pathway was identified as the core secondary metabolic pathway in response to allelopathic stress. This pathway relies on a series of enzymatic reactions catalyzed by key genes including phenylalanine ammonia-lyase (PAL), phenylalanine/tyrosine ammonia-lyase (PTAL), cinnamyl alcohol dehydrogenase (CAD) and cinnamoyl-CoA reductase (CCR), together with key metabolites such as p-Coumaric acid, Ferulic acid and Sinapyl alcohol, to produce metabolic products including lignin and flavonoids. This study provides a theoretical basis for revealing the molecular mechanism underlying the allelopathic response of Elymus nutans to the extracts of Ligularia sagitta, and also offers a scientific basis for the conservation and sustainable utilization of grassland ecosystems in alpine regions.