Multi-Omics Profiling Unveils Antifungal Secondary Metabolites Mediating Epicoccum layuense LQ’s Biocontrol Efficacy Against Colletotrichum fructicola

Colletotrichum fructicola is a significant phytopathogen in both pre- and postharvest stages of fruit development and storage. The development of environmentally-friendly biological control agents has attracted increasing research interest. In this study, we characterized a fungal strain (Epicoccum layuense LQ) that strongly inhibits C. fructicola. Potato dextrose broth culture filtrate of strain LQ inhibited vegetative growth of C. fructicola by approximately 80% at 1:10 (v/v) dilution. Cytological observations revealed that the filtrate disrupted mitosis and cellular polarity during conidial germination. Furthermore, the culture filtrate effectively suppressed C. fructicola infection on both apple leaves and fruits. The fungal strain LQ was identified as E. layuense through integrated morphological characterization and multi-locus phylogenetic analysis. Whole genome sequencing of strain LQ identified 36 biosynthetic gene clusters (BGCs), subsequent gene synteny analysis demonstrated structural conservation in three BGCs homologous to known antifungal clusters. Notably, substitution of NaNO3 with yeast extract in Czapek-Dox medium enhanced the antifungal activity of strain LQ filtrate by 14.2-fold. Consistent with this finding, transcriptomic profiling revealed significant upregulation of BGCs associated with epipyrone A and burnettramic acid A biosynthesis under yeast extract supplementation condition. In sum, our results demonstrate the antagonistic potential of E. layuense LQ and identify two candidate BGCs that may mediate this biocontrol activity, which lays a foundation for further mechanism dissection.