Giant transposable elements drive genetic diversification in Aspergillus oryzae, a domesticated fungus traditionally used in food fermentation

Starships are giant transposable elements recently reported in fungi that carry cargo genes and drive rapid adaptation. While inter-species variation by Starships has been investigated, their role in intra-species variation remains unclear. Here, we investigated Starships in Aspergillus oryzae , a filamentous fungus differentiated from mycotoxigenic Aspergillus flavus and subsequently domesticated for various applications in food fermentation, such as sake, miso , and soy sauce production in Japan. Comparative analysis between A . flavus and A . oryzae revealed that cargo gene gains/losses during domestication likely contribute to safe and stable food production. Furthermore, cargo gene composition varied even among A . oryzae strains harboring the same Starship classes, suggesting its correlation with specific strain usage. These findings indicate that Starships facilitate rapid evolution and diversification under artificial selection by acquiring and rearranging cargo genes. Our study highlights Starships as key vehicles driving genetic diversification in the domestication of A . oryzae for multipurpose industrial applications.