Abstract
In this study, the whole genome of Monascus ruber KACC 46666 was generated using the PacBio RSII sequencer with high-quality de novo assembly to obtain trustworthy assembly and annotation using genome assemblies with long reads from PacBio single-molecule real-time sequencing. The whole genome of M. ruber has a total length of 25.9 Mb, divided in 13 contigs with 9639 genes. The functions of genes involved in secondary metabolite production were further analyzed. Gene clusters involved in the production of Monascus pigment, monacolin K, and mycotoxin citrinin were identified. Notably, most of the citrinin gene cluster was lost, as confirmed via high-performance liquid chromatography analysis. This genome-level safety evaluation of industrially important Monascus strains will provide valuable information for genome-based microbial engineering of natural food colorants and production of commercially important secondary metabolites such as monacolin K.