Omics-Based Comparison of Fungal Virulence Genes, Biosynthetic Gene Clusters, and Small Molecules in <i>Penicillium expansum</i> and <i>Penicillium chrysogenum</i>
<i>Penicillium expansum</i> is a ubiquitous pathogenic fungus that causes blue mold decay of apple fruit postharvest, and another member of the genus, <i>Penicillium chrysogenum</i>, is a well-studied saprophyte valued for antibiotic and small molecule production. While these...
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2024-12-01
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| author | Holly P. Bartholomew Christopher Gottschalk Bret Cooper Michael R. Bukowski Ronghui Yang Verneta L. Gaskins Dianiris Luciano-Rosario Jorge M. Fonseca Wayne M. Jurick |
| author_facet | Holly P. Bartholomew Christopher Gottschalk Bret Cooper Michael R. Bukowski Ronghui Yang Verneta L. Gaskins Dianiris Luciano-Rosario Jorge M. Fonseca Wayne M. Jurick |
| author_sort | Holly P. Bartholomew |
| collection | DOAJ |
| description | <i>Penicillium expansum</i> is a ubiquitous pathogenic fungus that causes blue mold decay of apple fruit postharvest, and another member of the genus, <i>Penicillium chrysogenum</i>, is a well-studied saprophyte valued for antibiotic and small molecule production. While these two fungi have been investigated individually, a recent discovery revealed that <i>P. chrysogenum</i> can block <i>P. expansum-</i>mediated decay of apple fruit. To shed light on this observation, we conducted a comparative genomic, transcriptomic, and metabolomic study of two <i>P. chrysogenum</i> (404 and 413) and two <i>P. expansum</i> (Pe21 and R19) isolates. Global transcriptional and metabolomic outputs were disparate between the species, nearly identical for <i>P. chrysogenum</i> isolates, and different between <i>P. expansum</i> isolates. Further, the two <i>P. chrysogenum</i> genomes revealed secondary metabolite gene clusters that varied widely from <i>P. expansum</i>. This included the absence of an intact patulin gene cluster in <i>P. chrysogenum</i>, which corroborates the metabolomic data regarding its inability to produce patulin. Additionally, a core subset of <i>P. expansum</i> virulence gene homologues were identified in <i>P. chrysogenum</i> and were similarly transcriptionally regulated in vitro. Molecules with varying biological activities, and phytohormone-like compounds were detected for the first time in <i>P. expansum</i> while antibiotics like penicillin G and other biologically active molecules were discovered in <i>P. chrysogenum</i> culture supernatants. Our findings provide a solid omics-based foundation of small molecule production in these two fungal species with implications in postharvest context and expand the current knowledge of the <i>Penicillium</i>-derived chemical repertoire for broader fundamental and practical applications. |
| format | Article |
| id | doaj-art-6fb875e83a7a45918170ee0edfbc69a3 |
| institution | Kabale University |
| issn | 2309-608X |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
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| series | Journal of Fungi |
| spelling | doaj-art-6fb875e83a7a45918170ee0edfbc69a32025-01-24T13:37:13ZengMDPI AGJournal of Fungi2309-608X2024-12-011111410.3390/jof11010014Omics-Based Comparison of Fungal Virulence Genes, Biosynthetic Gene Clusters, and Small Molecules in <i>Penicillium expansum</i> and <i>Penicillium chrysogenum</i>Holly P. Bartholomew0Christopher Gottschalk1Bret Cooper2Michael R. Bukowski3Ronghui Yang4Verneta L. Gaskins5Dianiris Luciano-Rosario6Jorge M. Fonseca7Wayne M. Jurick8Food Quality Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USAInnovative Fruit Production, Improvement, and Protection, Appalachian Fruit Research Station, U.S. Department of Agriculture, Agricultural Research Service, Kearneysville, WV 25430, USASoybean Genomics and Improvement Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USAMethods and Application of Food Composition Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, MD 20705, USASoybean Genomics and Improvement Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USAFood Quality Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USAFood Quality Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USAFood Quality Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USAFood Quality Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA<i>Penicillium expansum</i> is a ubiquitous pathogenic fungus that causes blue mold decay of apple fruit postharvest, and another member of the genus, <i>Penicillium chrysogenum</i>, is a well-studied saprophyte valued for antibiotic and small molecule production. While these two fungi have been investigated individually, a recent discovery revealed that <i>P. chrysogenum</i> can block <i>P. expansum-</i>mediated decay of apple fruit. To shed light on this observation, we conducted a comparative genomic, transcriptomic, and metabolomic study of two <i>P. chrysogenum</i> (404 and 413) and two <i>P. expansum</i> (Pe21 and R19) isolates. Global transcriptional and metabolomic outputs were disparate between the species, nearly identical for <i>P. chrysogenum</i> isolates, and different between <i>P. expansum</i> isolates. Further, the two <i>P. chrysogenum</i> genomes revealed secondary metabolite gene clusters that varied widely from <i>P. expansum</i>. This included the absence of an intact patulin gene cluster in <i>P. chrysogenum</i>, which corroborates the metabolomic data regarding its inability to produce patulin. Additionally, a core subset of <i>P. expansum</i> virulence gene homologues were identified in <i>P. chrysogenum</i> and were similarly transcriptionally regulated in vitro. Molecules with varying biological activities, and phytohormone-like compounds were detected for the first time in <i>P. expansum</i> while antibiotics like penicillin G and other biologically active molecules were discovered in <i>P. chrysogenum</i> culture supernatants. Our findings provide a solid omics-based foundation of small molecule production in these two fungal species with implications in postharvest context and expand the current knowledge of the <i>Penicillium</i>-derived chemical repertoire for broader fundamental and practical applications.https://www.mdpi.com/2309-608X/11/1/14appleblue mold<i>Penicillium expansum</i><i>Penicillium chrysogenum</i>metabolomicssecondary metabolites |
| spellingShingle | Holly P. Bartholomew Christopher Gottschalk Bret Cooper Michael R. Bukowski Ronghui Yang Verneta L. Gaskins Dianiris Luciano-Rosario Jorge M. Fonseca Wayne M. Jurick Omics-Based Comparison of Fungal Virulence Genes, Biosynthetic Gene Clusters, and Small Molecules in <i>Penicillium expansum</i> and <i>Penicillium chrysogenum</i> Journal of Fungi apple blue mold <i>Penicillium expansum</i> <i>Penicillium chrysogenum</i> metabolomics secondary metabolites |
| title | Omics-Based Comparison of Fungal Virulence Genes, Biosynthetic Gene Clusters, and Small Molecules in <i>Penicillium expansum</i> and <i>Penicillium chrysogenum</i> |
| title_full | Omics-Based Comparison of Fungal Virulence Genes, Biosynthetic Gene Clusters, and Small Molecules in <i>Penicillium expansum</i> and <i>Penicillium chrysogenum</i> |
| title_fullStr | Omics-Based Comparison of Fungal Virulence Genes, Biosynthetic Gene Clusters, and Small Molecules in <i>Penicillium expansum</i> and <i>Penicillium chrysogenum</i> |
| title_full_unstemmed | Omics-Based Comparison of Fungal Virulence Genes, Biosynthetic Gene Clusters, and Small Molecules in <i>Penicillium expansum</i> and <i>Penicillium chrysogenum</i> |
| title_short | Omics-Based Comparison of Fungal Virulence Genes, Biosynthetic Gene Clusters, and Small Molecules in <i>Penicillium expansum</i> and <i>Penicillium chrysogenum</i> |
| title_sort | omics based comparison of fungal virulence genes biosynthetic gene clusters and small molecules in i penicillium expansum i and i penicillium chrysogenum i |
| topic | apple blue mold <i>Penicillium expansum</i> <i>Penicillium chrysogenum</i> metabolomics secondary metabolites |
| url | https://www.mdpi.com/2309-608X/11/1/14 |
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