Black Aspergillus luchuensis and its white albino mutant are essential fungi for making alcoholic beverages in Japan. A large number of industrial strains have been created using novel isolation or gene/genome mutation techniques. Such mutations influence metabolic and phenotypic characteristics in industrial strains, but few comparative studies of inter-strain mutation have been conducted.

We carried out comparative genome analyses of 8 industrial strains of A. luchuensis and A. kawachii IFO 4308, the latter being the first albino strain to be isolated. Phylogenetic analysis based on 8938 concatenated genes exposed the diversity of black koji strains and uniformity among albino industrial strains, suggesting that passaged industrial albino strains have more genetic mutations compared with strain IFO 4308 and black koji strains.

Comparative analysis showed that the albino strains had mutations in genes not only for conidial pigmentation but also in those that encode N-terminal acetyltransferase A and annexin XIV-like protein. The results also suggest that some mutations may have emerged through subculturing of albino strains. For example, mutations in the genes for isocitrate lyase and sugar transporters were observed only in industrial albino strains. This implies that selective pressure for increasing enzyme activity or secondary metabolites may have influenced the mutation of genes associated with environmental stress responses in A. luchuensis albino strains.

Our study clarifies hitherto unknown genetic and metabolic characteristics of A. luchuensis industrial strains and provides potential applications for comparative genome analysis for breeding koji strains.

黑曲霉及其白色白变种是日本制造酒精饮料的必需真菌。已经使用新的分离或基因/基因组突变技术创建了大量工业菌株。这种突变会影响工业菌株的代谢和表型特征，但很少有关于菌株间突变的比较研究。

我们对 8 个工业菌株A. luchuensis和A. kawachii IFO 4308进行了比较基因组分析，后者是第一个被分离的白化菌株。基于8938个连锁基因的系统发育分析揭示了黑曲菌株的多样性和白化工业菌株之间的一致性，表明与菌株IFO 4308和黑曲菌株相比，传代的工业白化菌株具有更多的基因突变。

比较分析表明，白化菌株不仅在分生孢子色素沉着的基因中发生突变，而且在编码 N 末端乙酰转移酶 A 和膜联蛋白 XIV 样蛋白的基因中也发生突变。结果还表明，一些突变可能是通过白化菌株的继代培养而出现的。例如，异柠檬酸裂合酶和糖转运蛋白基因的突变仅在工业白化菌株中观察到。这意味着增加酶活性或次生代谢物的选择压力可能影响了与A. luchuensis白化菌株中与环境应激反应相关的基因突变。

我们的研究阐明了迄今为止未知的A. luchuensis工业菌株的遗传和代谢特征，并为育种酒曲菌株的比较基因组分析提供了潜在应用。