Population-Specific Transcriptomic Shifts Underlie Secondary Metabolic Diversification in Aspergillus flavus and the Domestication of Aspergillus oryzae

The genomic signatures of microbial domestication remain poorly understood within the context of natural population variation. Here, we demonstrate that Aspergillus oryzae, the filamentous fungus used in soy sauce production, shares more recent ancestry with a predominantly northern, largely non-aflatoxigenic population of Aspergillus flavus (population C). Strikingly, A. oryzae isolates also overlap with the recently described, clinically enriched A. flavus population D, suggesting the possibility of multiple domestication events. Although A. oryzae exhibits reduced virulence compared to A. flavus, all isolates tested retained pathogenicity in a zebrafish infection model. At the transcriptomic level, Aspergillus populations are significantly differentiated, with distinct responses to population density, indicating that population-specific transcriptomes adapt differently to ecological conditions. These differences extend beyond gene content and are not always explained by phylogenetic relationships, suggesting that phenotypic diversification occurs through the rapid reorganization of transcriptomic architectures. For example, A. oryzae displays significantly elevated expression of a module enriched for carbohydrate metabolism. Population-specific variation is also evident among secondary metabolite (SM) gene clusters. While A. oryzae shows markedly reduced expression of specific SM genes, particularly those involved in aflatoxin biosynthesis, this trend does not extend across the entire secondary metabolome. Using machine- learning-based gene regulatory network inference, we identified population-specific transcriptomic differences linked to distinct transcription factors, with evidence for both cis- and trans-acting regulatory divergence, but no changes in global regulators such as laeA. Together, these findings provide new insights into the domestication of A. oryzae, its global significance, and the microevolution of fungal secondary metabolic pathways. Significance StatementAspergillus flavus poses a significant threat to global agriculture by infecting crops and producing aflatoxin, a potent carcinogen that undermines food safety and international trade. The species is also a major human pathogen causing invasive fungal infections. Here, we demonstrate that A. flavus populations exhibit not only variations in their capacity to produce toxins but also in the way they regulate gene expression in response to environmental cues. These regulatory differences played a key role in the domestication of Aspergillus oryzae, a non-aflatoxigenic relative that has been safely used in food fermentation for centuries. Notably, while A. oryzae exhibits reduced aflatoxin biosynthetic gene expression, it expresses other secondary metabolite genes and retains limited opportunistic pathogenic potential. By revealing how transcriptomic rewiring drives population-level divergence, this work provides new insights into the evolution of toxin production, with broad implications for microbial domestication, crop protection, and global food security.