Genomic and Metabolomic Analysis of the Endophytic Fungus <i>Fusarium</i> sp. VM-40 Isolated from the Medicinal Plant <i>Vinca minor</i>
The genus <i>Fusarium</i> is well-known to comprise many pathogenic fungi that affect cereal crops worldwide, causing severe damage to agriculture and the economy. In this study, an endophytic fungus designated <i>Fusarium</i> sp. VM-40 was isolated from a healthy specimen of...
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MDPI AG
2023-06-01
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| Series: | Journal of Fungi |
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| Online Access: | https://www.mdpi.com/2309-608X/9/7/704 |
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| author | Ting He Xiao Li Riccardo Iacovelli Thomas Hackl Kristina Haslinger |
| author_facet | Ting He Xiao Li Riccardo Iacovelli Thomas Hackl Kristina Haslinger |
| author_sort | Ting He |
| collection | DOAJ |
| description | The genus <i>Fusarium</i> is well-known to comprise many pathogenic fungi that affect cereal crops worldwide, causing severe damage to agriculture and the economy. In this study, an endophytic fungus designated <i>Fusarium</i> sp. VM-40 was isolated from a healthy specimen of the traditional European medicinal plant <i>Vinca minor</i>. Our morphological characterization and phylogenetic analysis reveal that <i>Fusarium</i> sp. VM-40 is closely related to <i>Fusarium paeoniae,</i> belonging to the <i>F. tricinctum</i> species complex (FTSC), the genomic architecture and secondary metabolite profile of which have not been investigated. Thus, we sequenced the whole genome of <i>Fusarium</i> sp. VM-40 with the new Oxford Nanopore R10.4 flowcells. The assembled genome is 40 Mb in size with a GC content of 47.72%, 15 contigs (≥50,000 bp; N 50~4.3 Mb), and 13,546 protein-coding genes, 691 of which are carbohydrate-active enzyme (CAZyme)-encoding genes. We furthermore predicted a total of 56 biosynthetic gene clusters (BGCs) with antiSMASH, 25 of which showed similarity with known BGCs. In addition, we explored the potential of this fungus to produce secondary metabolites through untargeted metabolomics. Our analyses reveal that this fungus produces structurally diverse secondary metabolites of potential pharmacological relevance (alkaloids, peptides, amides, terpenoids, and quinones). We also employed an epigenetic manipulation method to activate cryptic BGCs, which led to an increased abundance of several known compounds and the identification of several putative new compounds. Taken together, this study provides systematic research on the whole genome sequence, biosynthetic potential, and metabolome of the endophytic fungus <i>Fusarium</i> sp. VM-40. |
| first_indexed | 2024-03-11T00:55:47Z |
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| language | English |
| last_indexed | 2024-03-11T00:55:47Z |
| publishDate | 2023-06-01 |
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| spelling | doaj.art-7cfa4d5248f44db3ad8292d11673f7062023-11-18T20:01:10ZengMDPI AGJournal of Fungi2309-608X2023-06-019770410.3390/jof9070704Genomic and Metabolomic Analysis of the Endophytic Fungus <i>Fusarium</i> sp. VM-40 Isolated from the Medicinal Plant <i>Vinca minor</i>Ting He0Xiao Li1Riccardo Iacovelli2Thomas Hackl3Kristina Haslinger4Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The NetherlandsDepartment of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The NetherlandsDepartment of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The NetherlandsGroningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The NetherlandsDepartment of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The NetherlandsThe genus <i>Fusarium</i> is well-known to comprise many pathogenic fungi that affect cereal crops worldwide, causing severe damage to agriculture and the economy. In this study, an endophytic fungus designated <i>Fusarium</i> sp. VM-40 was isolated from a healthy specimen of the traditional European medicinal plant <i>Vinca minor</i>. Our morphological characterization and phylogenetic analysis reveal that <i>Fusarium</i> sp. VM-40 is closely related to <i>Fusarium paeoniae,</i> belonging to the <i>F. tricinctum</i> species complex (FTSC), the genomic architecture and secondary metabolite profile of which have not been investigated. Thus, we sequenced the whole genome of <i>Fusarium</i> sp. VM-40 with the new Oxford Nanopore R10.4 flowcells. The assembled genome is 40 Mb in size with a GC content of 47.72%, 15 contigs (≥50,000 bp; N 50~4.3 Mb), and 13,546 protein-coding genes, 691 of which are carbohydrate-active enzyme (CAZyme)-encoding genes. We furthermore predicted a total of 56 biosynthetic gene clusters (BGCs) with antiSMASH, 25 of which showed similarity with known BGCs. In addition, we explored the potential of this fungus to produce secondary metabolites through untargeted metabolomics. Our analyses reveal that this fungus produces structurally diverse secondary metabolites of potential pharmacological relevance (alkaloids, peptides, amides, terpenoids, and quinones). We also employed an epigenetic manipulation method to activate cryptic BGCs, which led to an increased abundance of several known compounds and the identification of several putative new compounds. Taken together, this study provides systematic research on the whole genome sequence, biosynthetic potential, and metabolome of the endophytic fungus <i>Fusarium</i> sp. VM-40.https://www.mdpi.com/2309-608X/9/7/704endophytic fungus<i>Fusarium</i> sp. VM-40whole genome sequencemetabolomicsbiosynthetic gene clustersmolecular networking |
| spellingShingle | Ting He Xiao Li Riccardo Iacovelli Thomas Hackl Kristina Haslinger Genomic and Metabolomic Analysis of the Endophytic Fungus <i>Fusarium</i> sp. VM-40 Isolated from the Medicinal Plant <i>Vinca minor</i> Journal of Fungi endophytic fungus <i>Fusarium</i> sp. VM-40 whole genome sequence metabolomics biosynthetic gene clusters molecular networking |
| title | Genomic and Metabolomic Analysis of the Endophytic Fungus <i>Fusarium</i> sp. VM-40 Isolated from the Medicinal Plant <i>Vinca minor</i> |
| title_full | Genomic and Metabolomic Analysis of the Endophytic Fungus <i>Fusarium</i> sp. VM-40 Isolated from the Medicinal Plant <i>Vinca minor</i> |
| title_fullStr | Genomic and Metabolomic Analysis of the Endophytic Fungus <i>Fusarium</i> sp. VM-40 Isolated from the Medicinal Plant <i>Vinca minor</i> |
| title_full_unstemmed | Genomic and Metabolomic Analysis of the Endophytic Fungus <i>Fusarium</i> sp. VM-40 Isolated from the Medicinal Plant <i>Vinca minor</i> |
| title_short | Genomic and Metabolomic Analysis of the Endophytic Fungus <i>Fusarium</i> sp. VM-40 Isolated from the Medicinal Plant <i>Vinca minor</i> |
| title_sort | genomic and metabolomic analysis of the endophytic fungus i fusarium i sp vm 40 isolated from the medicinal plant i vinca minor i |
| topic | endophytic fungus <i>Fusarium</i> sp. VM-40 whole genome sequence metabolomics biosynthetic gene clusters molecular networking |
| url | https://www.mdpi.com/2309-608X/9/7/704 |
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