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Safety evaluation of mycotoxin citrinin production from Monascus ruber through whole-genome sequencing and analytical evaluation


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.

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Data availability

The whole-genome sequence of a wild-type M. ruber strain (KACC 46666) was deposited in the National Center for Biotechnology Information (NCBI) database under the accession number JAMZNN000000000 (BioProject accession code PRJNA749921). The raw sequencing data are available at the Sequence Read Archive database of NCBI (accessions: SRX11561645-SRX11561649).


  • Aamir S (2015) A rapid and efficient method of fungal genomic DNA extraction, suitable for PCR based molecular methods. Plant Pathol Quar 5(2):74–81

    Article  Google Scholar 

  • Alberts AW (1988) Discovery, biochemistry and biology of lovastatin. Am J Cardiol 62(15):10J-15J

    CAS  Article  Google Scholar 

  • Barbosa RN, Leong SL, Vinnere-Pettersson O, Chen AJ, Souza-Motta CM, Frisvad JC, Samson RA, Oliveira NT, Houbraken J (2017) Phylogenetic analysis of Monascus and new species from honey, pollen and nests of stingless bees. Stud Mycol 86:29–51

    CAS  Article  Google Scholar 

  • Chen WP, He Y, Zhou YX, Shao YC, Feng YL, Li M, Chen FS (2015) Edible filamentous fungi from the species Monascus: early traditional fermentations, modern molecular biology, and future genomics. Compr Rev Food Sci Food Saf 14(5):555–567

    CAS  Article  Google Scholar 

  • Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10(6):563–569

    CAS  Article  Google Scholar 

  • Endo A (1979) Monacolin K, a new hypocholesterolemic agent produced by a Monascus species. J Antibiot (tokyo) 32(8):852–854

    CAS  Article  Google Scholar 

  • Feng YL, Shao YC, Zhou YX, Chen FS (2014) Monacolin K production by citrinin-free Monascus pilosus MS-1 and fermentation process monitoring. Eng Life Sci 14(5):538–545

    CAS  Article  Google Scholar 

  • Fu GM, Xu Y, Li YP, Tan WH (2007) Construction of a replacement vector to disrupt pksCT gene for the mycotoxin citrinin biosynthesis in Monascus aurantiacus and maintain food red pigment production. Asia Pac J Clin Nutr 16(supplement 1):137–142

    CAS  PubMed  Google Scholar 

  • He Y, Cox RJ (2016) The molecular steps of citrinin biosynthesis in fungi. Chem Sci 7(3):2119–2127

    CAS  Article  Google Scholar 

  • Higa Y, Kim YS, Altaf-Ul-Amin M, Huang M, Ono N, Kanaya S (2020) Divergence of metabolites in three phylogenetically close Monascus species (M. pilosus, M. ruber, and M. purpureus) based on secondary metabolite biosynthetic gene clusters. BMC Genom 21(1):679

    CAS  Article  Google Scholar 

  • Jones MG (2007) The first filamentous fungal genome sequences: Aspergillus leads the way for essential everyday resources or dusty museum specimens? Microbiology 153:1–6

    CAS  Article  Google Scholar 

  • Kim HJ, Ji GE, Lee I (2007) Natural occurring levels of citrinin and monacolin K in Korean Monascus fermentation products. Food Sci Biotechnol 16(1):142–145

    Google Scholar 

  • Li YP, Pan YF, Zou LH, Xu Y, Huang ZB, He QH (2013) Lower citrinin production by gene disruption of ctnB involved in citrinin biosynthesis in Monascus aurantiacus Li AS3.4384. J Agric Food Chem 61(30):7397–7402

    CAS  Article  Google Scholar 

  • Liang B, Du XJ, Li P, Sun CC, Wang S (2018) Investigation of citrinin and pigment biosynthesis mechanisms in Monascus purpureus by transcriptomic analysis. Front Microbiol 9:1374

    Article  Google Scholar 

  • Liu LJ, Zhao JX, Huang YL, Xin Q, Wang ZL (2018) Diversifying of chemical structure of native Monascus pigments. Front Microbiol 9:3143

    Article  Google Scholar 

  • Ma J, Li Y, Ye Q, Li J, Hua Y, Ju D, Zhang D, Cooper R, Chang M (2000) Constituents of red yeast rice, a traditional Chinese food and medicine. J Agric Food Chem 48(11):5220–5225

    CAS  Article  Google Scholar 

  • Meerpoel C, Vidal A, Andjelkovic M, De Boevre M, Tangni EK, Huybrechts B, Devreese M, Croubels S, De Saeger S (2021) Dietary exposure assessment and risk characterization of citrinin and ochratoxin A in Belgium. Food Chem Toxicol 147:111914

    CAS  Article  Google Scholar 

  • Patakova P (2013) Monascus secondary metabolites: production and biological activity. J Ind Microbiol Biotechnol 40(2):169–181

    CAS  Article  Google Scholar 

  • Shimizu T, Kinoshita H, Nihira T (2007) Identification and in vivo functional analysis by gene disruption of ctnA, an activator gene involved in citrinin biosynthesis in Monascus purpureus. Appl Environ Microbiol 73(16):5097–5103

    CAS  Article  Google Scholar 

  • Zhu B, Qi F, Wu J, Yin G, Hua J, Zhang Q, Qin L (2019) Red yeast rice: a systematic review of the traditional uses, chemistry, pharmacology, and quality control of an important Chinese folk medicine. Front Pharmacol 10:1449

    CAS  Article  Google Scholar 

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This work was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education [NRF-2021R1F1A1058927] and the Ministry of Science and ICT [NRF-2021M1A5A1075524] [KOPRI-PN22014]. The M. ruber KACC 46666 strain was kindly offered by Korean Agricultural Culture Collection (KACC).

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Authors and Affiliations



Conceptualization, HRY, YK, and HJK; methodology, HRY, YK, and HJK; validation, HRY, YK, and HJK; formal analysis, HRY, YK, and HJK; data curation, HRY, YK, SH and HJK; writing—original draft preparation, HRY, YK, and HJK; writing—review and editing, SCS and HJK; visualization, HRY, YK, SH, SCS and HJK; supervision, HJK; project administration, HJK; funding acquisition, HJK.

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Correspondence to Hyo Jin Kim.

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The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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Yoon, H.R., Ku, D., Han, S. et al. Safety evaluation of mycotoxin citrinin production from Monascus ruber through whole-genome sequencing and analytical evaluation. 3 Biotech 12, 214 (2022).

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  • Monascus ruber
  • Whole-genome sequencing
  • Citrinin
  • Fungal metabolites