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<div>The contamination of maize and peanut with aflatoxin during <i>Aspergillus flavus</i> infection is exacerbated by drought stress. This is correlated with the accumulation of reactive oxygen species (ROS) in host tissues. These ROS also stimulate the production of aflatoxin by <i>A. flavus</i>, which is postulated to provide fringe antioxidant benefits. In order to investigate the functional causes for isolate-to-isolate variation in oxidative stress responses and to characterize components pertinent to host resistance, 10 field isolates of <i>A. flavus</i> and <i>A. parasiticus</i> were used for whole genome re-sequencing (WGRS). Sequencing reads were aligned to the NRRL3357 reference genome with an average of 86.6X coverage for each isolate. Variant calling between the re-sequenced isolates and the reference genome found that toxigenic isolates exhibited fewer non-synonymous single nucleotide polymorphisms (SNPs) than atoxigenic isolates with averages of 22,601 and 34,294, respectively. Also, greater numbers of non-synonymous SNPs were observed than synonymous SNPs suggesting possible niche specialization in progress proportional to observed stress tolerance. Gene family variant enrichment analysis and variant influences on gene expression are under investigation. Understanding the factors influencing <i>A. flavus</i> stress responses and aflatoxin production will allow for targeted enhancement of host resistance through breeding, and the application of novel biotechnologies.</div>