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Background  Species of the genus  Monascus  are considered to be economically important and have been widely used in the production of yellow and red food colorants. In particular, three  Monascus  species, namely,  M. pilosus ,  M. purpureus , and  M. 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 by  M. pilosus  NBRC4520,  M. purpureus  NBRC4478 and  M. ruber  NBRC4483, 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 three  Monascus  species ( M. pilosus ,  M. purpureus , and  M. ruber ) at both the metabolome level by LCMS analysis and at the genome level. Specifically,  M. pilosus  NBRC4520,  M. purpureus  NBRC4478 and  M. ruber  NBRC4483 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 three  Monascus  species also diverged, confirming that  M. pilosus  and  M. purpureus  are chemotaxonomically different.  M. ruber  has similar biosynthetic and secondary metabolite gene clusters to  M. pilosus . The comparison of secondary metabolites produced also revealed divergence in the three species.    Conclusions  Our findings are important for improving the utilization of  Monascus  species in the food industry and industrial field. However, in view of food safety, we need to determine if the toxins produced by some  Monascus  strains exist in the genome or in the metabolome.

bmc genomics

Divergence of metabolites in three phylogenetically close Monascus species (M. pilosus, M. ruber, and M. purpureus) based on secondary metabolite biosynthetic gene clusters