Mycoviruses diversity in the black kōji mold, Aspergillus luchuensis (section Nigri) isolated from liquor-production environments in Japan

Some fungal species in the genus Aspergillus are economically important due to their role in the production of liquors and various foods; however, their viromes, which may affect their performance, remain unexplored. Therefore, this study examined the viromes of nine strains of Aspergillus luchuensis (section Nigri), the black kōji mold used in the production of shochu (a traditional Japanese liquor) in Japan. It identified virus-like sequences related to alterna-, partiti-, curvula, botourmia-, narna-like, and umbra-like viruses. Some sequences appear to represent new variants (e.g., alterna- and gammapartitiviruses), while many others correspond to novel viral species within established or proposed mycoviral families. All A. luchuensis strains harbored multiple virus infections, with 2 to 7 viruses per strain. Three alternavirus strains with four-segmented double-stranded RNA (dsRNA) genomes were confirmed, along with minor variants co-present with the predominant strains. Notably, a gammapartitivirus appears to have two additional dsRNA genome segments, along with two satellite-like short dsRNA segments in some fungal isolates. Furthermore, at least five short RNAs (0.48–1.31 kb) were identified, three of which are possibly satellite-like RNAs associated with novel single-stranded RNA viruses (botourmia- and umbra-like viruses). These findings reveal the great diversity of mycoviruses in A. luchuensis populations and lay the foundation for further investigation into their impact on fungal phenotypes and liquor production.