Comparative genomics of aflatoxigenic A. flavus reveals mycotoxin diversity and postharvest adaptation in cashew nuts from coastal Kenya.

Cashew is a key economic crop in coastal Kenya, yet its production faces significant challenges due to post-harvest fungal contamination, particularly by Aspergillus flavus and Aspergillus aculeatus. These fungi are known producers of mycotoxins, including aflatoxins, potent carcinogenic and mutagenic compounds that pose serious food safety and public health risks. Despite growing concerns, the genomic architecture, metabolic potential, and ecological adaptations of these fungi in cashew-growing regions remain poorly understood. This study investigated the genetic diversity, aflatoxin biosynthetic gene clusters (BGCs), secondary metabolite profiles, and carbohydrate-active enzyme (CAZyme) repertoires of aflatoxigenic A. flavus and compared them with non-aflatoxigenic A. aculeatus isolates obtained from cashew nuts collected in Kilifi, Kwale, and Lamu counties. A total of 18 fungal isolates (16 A. flavus, 2 A. aculeatus) were cultured and subjected to whole-genome sequencing using the Illumina platform. Genome mining and comparative analyses were performed using OrthoFinder, antiSMASH, and dbCAN. Phylogenomic analysis revealed five distinct clades among A. flavus isolates, suggesting substantial intraspecific diversity and potential regional adaptation, while A. aculeatus formed a single monophyletic clade. Comparative analysis of aflatoxin BGCs in A. flavus revealed notable structural variation, including gene deletions (aflT, omtA), insertions, and rearrangements, with conservation observed for core genes such as ordB, moxY, avfA, and adhA; however, the regulatory gene aflR was not conserved across all isolates. All the 2 A. aculeatus isolates lacked aflatoxin biosynthetic genes, indicating they are not aflatoxigenic. Both species harbored diverse SMBGCs, including PKS, NRPS, and strain-specific clusters such as YWA1, fusarin, and aspergillic acid, suggesting potential for co-production of multiple bioactive compounds. CAZyme profiling revealed abundant glycoside hydrolases and auxiliary activity enzymes, underscoring adaptation to pectin-rich cashew substrates. Despite similar genome sizes and GC content, species-specific differences in carbohydrate metabolism and secondary metabolite pathways indicate ecological plasticity. Our findings demonstrate that A. flavus and A. aculeatus populations in coastal Kenya are genetically diverse, metabolically versatile, and shaped by local environmental and anthropogenic pressures. The study provides essential genomic insights for region-specific aflatoxin risk assessment and highlights the need for careful screening of atoxigenic strains in biocontrol applications, as well as further exploration of cryptic BGCs and CAZyme functions in post-harvest fungal ecology.