Disruption of MAPK signalling and amino acid biosynthesis underlies the antifungal biocontrol mechanism of <i>Coniochaeta velutina</i> against <i>Colletotrichum gloeosporioides</i>: a transcriptome and metabolome analysis

<i>Colletotrichum gloeosporioides</i> is a destructive pathogen that causes significant economic and ecological losses in agricultural and forestry production. In search of effective biocontrol agents, this study isolated an endophytic fungus, <i>Coniochaeta velutina</i>, from healthy <i>Camellia oleifera</i> leaves and investigated its in vitro inhibitory mechanism on <i>Colletotrichum gloeosporioides</i> using transcriptomics and metabolomics analyses. These findings were used to evaluate the differences in gene expression and metabolite content between the treatment (<i>Coniochaeta velutina</i>-treated <i>Colletotrichum gloeosporioides</i>) and control (untreated <i>Colletotrichum gloeosporioides</i>) groups. The transcriptomic analysis detected a total of 15 310 expressed genes, with 3938 showing significant differential expression (<i>p</i> < 0.05) (2093 upregulated and 1845 downregulated genes). These genes were enriched primarily in the following pathways: mitogen-activated protein kinase (MAPK) signalling, antibiotic biosynthesis, amino acid metabolism, carbon metabolism, and peroxidase pathways. Metabolomic analysis revealed 452 metabolites in both groups, with 138 showing significant differences. These genes were enriched mainly in secondary metabolite biosynthesis, amino acid biosynthesis, and α-linolenic acid metabolism. Transcriptome and metabolome association analyses, along with qRT-PCR results, revealed that the levels of intracellular pectolinarigenin metabolites significantly increased in the treatment group, leading to disrupted MAPK signalling and reduced amino acid biosynthesis, which are essential for maintaining normal cell growth. Notably, the decrease in terpenoid compounds was the primary reason that <i>Colletotrichum gloeosporioides</i> was inhibited by the biocontrol fungus <i>Coniochaeta velutina.</i> Therefore, these findings provide valuable insights into the biocontrol mechanisms of <i>Coniochaeta velutina</i> against <i>Colletotrichum gloeosporioides</i> and offer a promising foundation for the development of new anthracnose prevention and control strategies.