Aspergillus oryzae, or 'Koji-kin' in Japanese, is one of the filamentous fungi most widely used in fermentation industries in Japan. It is exploited in the production of sake, 'miso' (soybean paste), 'shoyu' (soy sauce) etc. and has been safely used in more than 1,000 years. Hence, it is often called 'fungus of the country'. It can be used for large-scale production of enzymes and other proteins and is regarded as an ideal host for the synthesis of active proteins of eukaryotic origins that cannot be achieved with E. coli.

The 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and Aspergillus fumigatus. Comparison of the three Aspergillus species revealed the presence of syntenic blocks and A. oryzae-specific blocks (lacking synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.