Genomic and Metabolomic Investigation of Aspergillus flavus Diversity and Aflatoxin Regulation Mechanisms in Nigerian Agricultural Ecosystems

Aspergillus flavus, the primary producer of aflatoxins B1 and B2 in agricultural commodities, exhibits remarkable genomic and phenotypic diversity that fundamentally influences aflatoxin contamination risk across different agricultural ecosystems. Understanding this diversity in Nigerian-specific populations is critical for developing targeted biocontrol strategies and for designing molecular detection tools calibrated to locally relevant strains. This study conducted a comprehensive genomic and metabolomic investigation of Aspergillus flavus diversity and aflatoxin regulation mechanisms in agricultural ecosystems across Nigeria's three major agroecological zones. A collection of 186 Aspergillus flavus isolates was assembled from maize, groundnut, and sorghum samples collected from fifteen states representing North West, North East, North Central, South East, South West, and South South geopolitical zones. Whole-genome sequencing using Nanopore and Illumina short-read technologies was performed. Phylogenomic analysis, comparative genomics of the aflatoxin biosynthetic gene cluster, and pangenome construction were conducted. Untargeted metabolomics using liquid chromatography high-resolution mass spectrometry characterised secondary metabolite profiles. Population structure was modelled using principal component analysis and STRUCTURE software. Results revealed three phylogenetically distinct Nigerian Aspergillus flavus populations with differential aflatoxin-producing capacity correlated with accessory genome complement. Novel regulatory genes associated with atoxigenic phenotypes in two populations were identified, providing targets for biocontrol strain development. The study delivers the most comprehensive genomic atlas of Aspergillus flavus diversity in Nigeria and establishes a genomic basis for rational biocontrol strategy design. Keywords: Aspergillus flavus, genomics, aflatoxin biosynthesis, biocontrol, Nigeria.