Biosynthetic potential of the culturable foliar fungi associated with field-grown lettuce

Fungal endophytes and epiphytes associated with plant leaves can play important ecological roles through the production of specialized metabolites encoded by biosynthetic gene clusters (BGCs). However, their functional capacity, especially in crops like lettuce (Lactuca sativa L.), remains poorly understood. We sequenced the genomes of nine fungal isolates, representing Fusarium sp., Fulvia sp., Alternaria alternata, and Alternaria postmessia, from leaves of lettuce grown under field conditions in Arizona, USA. We used antibiotics and secondary metabolite analysis shell (antiSMASH) and the database for automated carbohydrate-active enzyme annotation (dbCAN3), to predict BGCs and carbohydrate-active enzymes (CAZymes) for each strain, and then compared them to conspecific strains from other environments and substrates. Foliar lettuce-associated fungi featured 39–95 BGCs per genome, with substantial overlap between isolates occurring in association with lettuce leaves vs. from other substrates. Species identity was a significant determinant of BGC count, while host type, isolation source, and lifestyle were not. Several BGCs, including those for alternariol and 1,3,6,8-Tetrahydroxynaphthalene (T4HN), showed 100% similarity to characterized minimum information about a biosynthetic gene cluster (MIBiG) clusters based on antiSMASH predictions. Although analysis by biosynthetic gene similarity clustering and prospecting engine (BiG-SCAPE) identified gene cluster families (GCFs) across the dataset, these reference-matching clusters were not always grouped, reflecting methodological differences in how the tools assess similarity. Comparative CAZyme analysis in a focal species (Fulvia sp.) revealed higher gene counts in a foliar lettuce-derived isolate than in tomato (Solanum lycopersicum)-associated strains, challenging assumptions about host chemical complexity. These results highlight the importance of phylogenetic context in shaping fungal functional potential and suggest that selection on microbial traits in edible leafy crops may be more subtle and species-specific than previously assumed.

• Lettuce-associated fungi feature diverse biosynthetic potential

• Phylogeny predicts fungal BGC content more strongly than ecological lifestyle

• Findings support genome-informed microbiome strategies for leafy crops