Genomic and transcriptomic study links A. oryzae to multiple A. flavus domestication events

A genomic and transcriptomic study reports that Aspergillus oryzae, the filamentous fungus used to produce soy sauce and sake, shares more recent ancestry with a predominantly northern, largely non-aflatoxigenic population of Aspergillus flavus called population C. The study’s abstract also describes overlap between A. oryzae isolates and the recently described, clinically enriched A. flavus population D, suggesting multiple domestication events rather than a single origin.

The researchers compared populations at the transcriptomic level and found significant differentiation, including different responses to spore density. Most expression variation followed relationships inferred from phylogeny, but some co-expression modules diverged more than expected from that evolutionary pattern. The authors interpret this as evidence that phenotypic diversification can sometimes involve reorganization of transcriptomic architecture. In A. oryzae, elevated expression of a carbohydrate-metabolism module was consistent with phylogenetic differentiation, leaving open whether enhanced carbohydrate metabolism began evolving before domestication or is most evident under fermentation-relevant conditions.

Secondary-metabolite gene clusters also varied among populations. Although A. oryzae showed markedly reduced expression of aflatoxin-biosynthesis genes, the abstract emphasizes that this pattern did not extend across the entire secondary metabolome. Machine-learning-based gene-regulatory-network inference linked population-specific expression differences to distinct transcription factors and provided evidence for both cis- and trans-acting regulatory divergence, while identifying no changes in global regulators such as laeA.

This was an experimental population study that included a zebrafish infection model: all isolates tested retained pathogenicity in that model, which does not establish effects in humans. The findings are summarized here from the supplied abstract, which does not provide sample sizes, statistical effect sizes, tested conditions or other details needed for a full assessment of the study’s scope and limitations.

Subject of Research: Population-specific genomic and transcriptomic variation associated with the domestication of Aspergillus oryzae

Article Title: Population-specific transcriptomic shifts underlie secondary metabolic diversification in Aspergillus flavus Link and the domestication of Aspergillus oryzae (Ahlb.)

Article References: Drott, M. T., Wang, Y.-W., Hatmaker, E. A., Mercado-Soto, N. M., Elmore, J. M., Luciano-Rosaro, D., Yu, J.-H., Rokas, A., Gibbons, J. G., Huttenlocher, A., Yang, K., & Keller, N. P. (2026). Population-specific transcriptomic shifts underlie secondary metabolic diversification in Aspergillus flavus Link and the domestication of Aspergillus oryzae (Ahlb.). IMA Fungus, 17, Article e195218. https://doi.org/10.3897/imafungus.17.195218

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.195218

Keywords: Aspergillus oryzae, Aspergillus flavus, fungal domestication, transcriptomics, secondary metabolism, aflatoxin genes, gene regulatory networks, genomic ancestry, zebrafish infection model, Population-specific, transcriptomic, shifts