Divergence of metabolites in three phylogenetically closeMonascusspecies (M. pilosus,M. ruber,andM. purpureus) based on secondary metabolite biosynthetic gene clusters

Background Species of the genusMonascusare considered to be economically important and have been widely used in the production of yellow and red food colorants. In particular, threeMonascusspecies, namely,M. pilosus,M. purpureus, andM. ruber, are used for food fermentation in the cuisine of East Asian countries such as China, Japan, and Korea. These species have also been utilized in the production of various kinds of natural pigments. However, there is a paucity of information on the genomes and secondary metabolites of these strains. Here, we report the genomic analysis and secondary metabolites produced byM. pilosusNBRC4520,M. purpureusNBRC4478 andM. ruberNBRC4483, which are NBRC standard strains. We believe that this report will lead to a better understanding of red yeast rice food. Results We examined the diversity of secondary metabolite production in threeMonascusspecies (M. pilosus,M. purpureus, andM. ruber) at both the metabolome level by LCMS analysis and at the genome level. Specifically,M. pilosusNBRC4520,M. purpureusNBRC4478 andM. ruberNBRC4483 strains were used in this study. Illumina MiSeq 300 bp paired-end sequencing generated 17 million high-quality short reads in each species, corresponding to 200 times the genome size. We measured the pigments and their related metabolites using LCMS analysis. The colors in the liquid media corresponding to the pigments and their related metabolites produced by the three species were very different from each other. The gene clusters for secondary metabolite biosynthesis of the threeMonascusspecies also diverged, confirming thatM. pilosusandM. purpureusare chemotaxonomically different.M. ruberhas similar biosynthetic and secondary metabolite gene clusters toM. pilosus. The comparison of secondary metabolites produced also revealed divergence in the three species. Conclusions Our findings are important for improving the utilization ofMonascusspecies in the food industry and industrial field. However, in view of food safety, we need to determine if the toxins produced by someMonascusstrains exist in the genome or in the metabolome.