{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T04:18:08Z","timestamp":1788236288037,"version":"build-2803163510"},"reference-count":30,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T00:00:00Z","timestamp":1788134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Shanghai State-owned Assets Supervision and Administration Commission Enterprise Innovation Development and Capacity Enhancement Program","award":["2022013"],"award-info":[{"award-number":["2022013"]}]},{"award":["2022013"],"award-info":[{"award-number":["2022013"]}],"id":[{"id":"https:\/\/ror.org\/004nx8f14","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Foods"],"abstract":"<jats:p>Monascus species are widely used in traditional fermented foods for pigment and flavor formation, but citrinin contamination remains a major safety concern that limits broader food applications. Therefore, this study aimed to evaluate the citrinin risk of a furu-derived Monascus ruber strain, BC20, by integrating phenotypic screening across food-relevant matrices with genome-resolved analysis. After 14 days of cultivation across eight matrices, including fungal media as well as dairy-, cereal-, and bran-based substrates, citrinin was not detected by immunoaffinity cleanup combined with HPLC\u2013FLD (LOD, 4 \u03bcg\/kg; LOQ, 12 \u03bcg\/kg). To investigate the genetic basis of this phenotype, we generated a chromosome-scale genome assembly for BC20 and conducted comparative analyses across a total of 19 Monascus genomes. ANI analysis and phylogenomic inference consistently placed BC20 within the ruber\u2013pilosus clade. Comparative synteny analysis showed that the citrinin-associated locus in BC20 no longer retained an intact cluster configuration but instead exhibited a remnant-locus architecture, and similar patterns were also observed in several related genomes from the same clade. By contrast, the monacolin K (mk) locus remained syntenically conserved in BC20, supporting locus-specific structural disturbance rather than assembly-derived pseudo-absence. Additionally, its antifungal susceptibility was determined. Overall, BC20 represents a M. ruber candidate strain with undetectable citrinin, and this study provides a practical analytical framework for citrinin risk screening in food-related Monascus isolates.<\/jats:p>","DOI":"10.3390\/foods15173091","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T03:19:26Z","timestamp":1788232766000},"page":"3091","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Chromosome-Scale Genome Analysis Reveals Locus-Specific Disruption of the Citrinin-Associated Region in a Furu-Derived Monascus ruber Strain BC20"],"prefix":"10.3390","volume":"15","author":[{"given":"Huanchang","family":"Zhang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Dairy Biotechnology, Key Laboratory of Functional Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd., Shanghai, 201103, China"},{"name":"Fudan Microbiome Center, School of Life Sciences, Fudan University, No. 2005 Songhu Road, Yangpu District, Shanghai 200438, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0983-2535","authenticated-orcid":false,"given":"Danqi","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Dairy Biotechnology, Key Laboratory of Functional Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd., Shanghai, 201103, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"}]},{"given":"Jin","family":"Han","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Dairy Biotechnology, Key Laboratory of Functional Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd., Shanghai, 201103, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Fenghua","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Dairy Biotechnology, Key Laboratory of Functional Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd., Shanghai, 201103, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"visualization","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-5264-1253","authenticated-orcid":false,"given":"Yiru","family":"Liu","sequence":"additional","affiliation":[{"name":"China Center of Industrial Culture Collection, China National Research Institute of Food & Fermentation Industries Corporation Limited, Beijing, 100015, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-6943-3860","authenticated-orcid":false,"given":"Rui","family":"Liu","sequence":"additional","affiliation":[{"name":"China Center of Industrial Culture Collection, China National Research Institute of Food & Fermentation Industries Corporation Limited, Beijing, 100015, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"}]},{"given":"Miya","family":"Su","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Dairy Biotechnology, Key Laboratory of Functional Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd., Shanghai, 201103, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"}]},{"given":"Su","family":"Yao","sequence":"additional","affiliation":[{"name":"China Center of Industrial Culture Collection, China National Research Institute of Food & Fermentation Industries Corporation Limited, Beijing, 100015, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3777-087X","authenticated-orcid":false,"given":"Zhenmin","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Dairy Biotechnology, Key Laboratory of Functional Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd., Shanghai, 201103, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Jiao, J., Zheng, Z., Liu, Z., and You, C. (2021). Study of the Compositional, Microbiological, Biochemical, and Volatile Profile of Red-Veined Cheese, an Internal Monascus-Ripened Variety. Front. Nutr., 8.","DOI":"10.3389\/fnut.2021.649611"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1021\/jf103652n","article-title":"Anti-tumor and anti-inflammatory properties of ankaflavin and monaphilone A from monascus purpureus NTU 568","volume":"59","author":"Hsu","year":"2011","journal-title":"J. Agric. Food Chem."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/j.ijbiomac.2014.03.020","article-title":"Retrograded maize starch used as a medium to enrich Monascus from the air in winter","volume":"67","author":"Liu","year":"2014","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"109657","DOI":"10.1016\/j.foodres.2020.109657","article-title":"Proteolysis, lipolysis, texture and sensory properties of cheese ripened by Monascus fumeus","volume":"137","author":"Xia","year":"2020","journal-title":"Food Res. Int."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Luo, A., Cheng, Z., Zhao, J., Hao, J., Shi, S., and Hu, B. (2023). The Relationship between Microbial Community Succession and Flavor Formation during the Natural Fermentation of Hongqu sufu. Foods, 12.","DOI":"10.3390\/foods12142800"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"128410","DOI":"10.1016\/j.foodchem.2020.128410","article-title":"Addition of genistein to the fermentation process reduces citrinin production by Monascus via changes at the transcription level","volume":"343","author":"Ouyang","year":"2021","journal-title":"Food Chem."},{"key":"ref_7","unstructured":"(2016). National Food Safety Standard\u2014Food Additive: Monascus Red (Standard No. GB 1886.181-2016)."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"5097","DOI":"10.1128\/AEM.01979-06","article-title":"Identification and in vivo functional analysis by gene disruption of ctnA, an activator gene involved in citrinin biosynthesis in Monascus purpureus","volume":"73","author":"Shimizu","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Higa, Y., Kim, Y.S., Altaf-Ul-Amin, M., Huang, M., Ono, N., and 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.","DOI":"10.1186\/s12864-020-06864-9"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"103687","DOI":"10.1016\/j.fgb.2022.103687","article-title":"Investigation of citrinin and monacolin K gene clusters variation among pigment producer Monascus species","volume":"160","author":"Liu","year":"2022","journal-title":"Fungal Genet. Biol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"85","DOI":"10.38212\/2224-6614.3438","article-title":"Investigation of monacolin K, yellow pigments, and citrinin production capabilities of Monascus purpureus and Monascus ruber (Monascus pilosus)","volume":"31","author":"Lin","year":"2023","journal-title":"J. Food Drug Anal."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Zhang, Z., Cui, M., Chen, P., Li, J., Mao, Z., Mao, Y., Li, Z., Guo, Q., Wang, C., and Liao, X. (2023). Insight into the phylogeny and metabolic divergence of Monascus species (M. pilosus, M. ruber, and M. purpureus) at the genome level. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1199144"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2119","DOI":"10.1039\/C5SC04027B","article-title":"The molecular steps of citrinin biosynthesis in fungi","volume":"7","author":"He","year":"2016","journal-title":"Chem. Sci."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1099\/mic.0.077628-0","article-title":"Physiological impact of transposable elements encoding DDE transposases in the environmental adaptation of Streptococcus agalactiae","volume":"160","author":"Gilot","year":"2014","journal-title":"Microbiology"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods","volume":"28","author":"Tamura","year":"2011","journal-title":"Mol. Biol. Evol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"W435","DOI":"10.1093\/nar\/gkl200","article-title":"AUGUSTUS: Ab initio prediction of alternative transcripts","volume":"34","author":"Stanke","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1101\/gr.1865504","article-title":"GeneWise and Genomewise","volume":"14","author":"Birney","year":"2004","journal-title":"Genome Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"R7","DOI":"10.1186\/gb-2008-9-1-r7","article-title":"Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments","volume":"9","author":"Haas","year":"2008","journal-title":"Genome Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"9077","DOI":"10.1093\/nar\/gkab688","article-title":"tRNAscan-SE 2.0: Improved detection and functional classification of transfer RNA genes","volume":"49","author":"Chan","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNAmmer: Consistent and rapid annotation of ribosomal RNA genes","volume":"35","author":"Lagesen","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2933","DOI":"10.1093\/bioinformatics\/btt509","article-title":"Infernal 1.1: 100-fold faster RNA homology searches","volume":"29","author":"Nawrocki","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes","volume":"38","author":"Manni","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1661","DOI":"10.1038\/s41592-023-02018-3","article-title":"Fast and robust metagenomic sequence comparison through sparse chaining with skani","volume":"20","author":"Shaw","year":"2023","journal-title":"Nat. Methods"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: Phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"btad121","DOI":"10.1093\/bioinformatics\/btad121","article-title":"NGenomeSyn: An easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes","volume":"39","author":"He","year":"2023","journal-title":"Bioinformatics"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Huang, Y., Yang, C., Moln\u00e1r, I., and Chen, S. (2023). Comparative Transcriptomic Analysis of Key Genes Involved in Citrinin Biosynthesis in Monascus purpureus. J. Fungi, 9.","DOI":"10.3390\/jof9020200"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Guo, X., Chen, K., Chen, L., Le, T.N., Zhao, M., and Cai, H. (2025). Effects of Cold Post-Fermentation Process on Microbial Diversity and Biogenic Amines in Protease-Assisted Fermented sufu. Foods, 14.","DOI":"10.3390\/foods14050735"}],"container-title":["Foods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/17\/3091\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T03:52:47Z","timestamp":1788234767000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2304-8158\/15\/17\/3091"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,31]]},"references-count":30,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["foods15173091"],"URL":"https:\/\/doi.org\/10.3390\/foods15173091","relation":{},"ISSN":["2304-8158"],"issn-type":[{"value":"2304-8158","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,31]]}}}