Aspergillus flavus La3279, a component strain of the Aflasafe T biocontrol product, contains a partial aflatoxin biosynthesis gene cluster followed by a genomic region highly variable among A. flavus isolates

Aspergillus flavus communities in agricultural fields consist of isolates with varying abilities to produce aflatoxins, which are highly toxic and carcinogenic to humans and animals. Biological control using multiple nonaflatoxigenic strains as a formulation to outcompete aflatoxigenic A. flavus has become a mainstream strategy. Aflasafe (TM) is a biocontrol product composed of four strains, Ka16127, La3279, La3304 and Og0222. It was first developed in Nigeria and is now widely used on maize and groundnut. In this study, phylogenetic analyses based on genome-wide single nucleotide polymorphisms showed that Ka16127 and La3304 were more closely related to each other than both were to La3279, and the three were distantly related to Og0222. Detailed molecular characterization of La3279 indicated that its genome, contradictory to the published report, lacked approximately half of the aflatoxin gene cluster as well as the entire cyclopiazonic acid gene cluster. La3279 was a member of the previously known "pattern E" group, which includes A. flavus and Aspergillus oryzae isolates that have the aforementioned deletion followed by a 3.8-kb "E block" sequence insertion. In comparison to the E block, corresponding regions in typical aflatoxigenic S-morphotype/genotype isolates as well as Ka16127 and La3304 were found to lack 1.1 kb of the 5' portion whereas L-morphotype/genotype isolates contained a complete nonhomologous region characterized by 2.5 copies of A. flavus telomeric repeat sequence at one end. Regions corresponding to the E block were highly variable and were useful for classifying A. flavus isolates into groups that mostly contained both mating types. The presence of both mating-type genes in genetically closely related A. flavus suggests a previously active sexual cycle. It could facilitate the development of a refined biocontrol strategy such as deploying biocontrol strains with the same mating-type that is predominant in a field A. flavus population.