Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events
Abstract The Penicillia are known to produce a wide range natural products—some with devastating outcome for the agricultural industry and others with unexploited potential in different applications. However, a large-scale overview of the biosynthetic potential of different species has been lacking....
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BMC
2023-02-01
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| Series: | IMA Fungus |
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| Online Access: | https://doi.org/10.1186/s43008-023-00108-7 |
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| author | Celine Petersen Trine Sørensen Mikkel R. Nielsen Teis E. Sondergaard Jens L. Sørensen David A. Fitzpatrick Jens C. Frisvad Kåre L. Nielsen |
| author_facet | Celine Petersen Trine Sørensen Mikkel R. Nielsen Teis E. Sondergaard Jens L. Sørensen David A. Fitzpatrick Jens C. Frisvad Kåre L. Nielsen |
| author_sort | Celine Petersen |
| collection | DOAJ |
| description | Abstract The Penicillia are known to produce a wide range natural products—some with devastating outcome for the agricultural industry and others with unexploited potential in different applications. However, a large-scale overview of the biosynthetic potential of different species has been lacking. In this study, we sequenced 93 Penicillium isolates and, together with eleven published genomes that hold similar assembly characteristics, we established a species phylogeny as well as defining a Penicillium pangenome. A total of 5612 genes were shared between ≥ 98 isolates corresponding to approximately half of the average number of genes a Penicillium genome holds. We further identified 15 lateral gene transfer events that have occurred in this collection of Penicillium isolates, which might have played an important role, such as niche adaption, in the evolution of these fungi. The comprehensive characterization of the genomic diversity in the Penicillium genus supersedes single-reference genomes, which do not necessarily capture the entire genetic variation. |
| format | Article |
| id | doaj-art-8363c83741584be79ebf37bffe69f3ce |
| institution | Kabale University |
| issn | 2210-6359 |
| language | English |
| publishDate | 2023-02-01 |
| publisher | BMC |
| record_format | Article |
| series | IMA Fungus |
| spelling | doaj-art-8363c83741584be79ebf37bffe69f3ce2025-02-02T14:35:55ZengBMCIMA Fungus2210-63592023-02-0114111710.1186/s43008-023-00108-7Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer eventsCeline Petersen0Trine Sørensen1Mikkel R. Nielsen2Teis E. Sondergaard3Jens L. Sørensen4David A. Fitzpatrick5Jens C. Frisvad6Kåre L. Nielsen7Department of Chemistry and Bioscience, Aalborg UniversityDepartment of Chemistry and Bioscience, Aalborg UniversityDepartment of Chemistry and Bioscience, Aalborg UniversityDepartment of Chemistry and Bioscience, Aalborg UniversityDepartment of Chemistry and Bioscience, Aalborg UniversityDepartment of Biology, Maynooth UniversityDepartment of Biotechnology and Biomedicine, Technical University of DenmarkDepartment of Chemistry and Bioscience, Aalborg UniversityAbstract The Penicillia are known to produce a wide range natural products—some with devastating outcome for the agricultural industry and others with unexploited potential in different applications. However, a large-scale overview of the biosynthetic potential of different species has been lacking. In this study, we sequenced 93 Penicillium isolates and, together with eleven published genomes that hold similar assembly characteristics, we established a species phylogeny as well as defining a Penicillium pangenome. A total of 5612 genes were shared between ≥ 98 isolates corresponding to approximately half of the average number of genes a Penicillium genome holds. We further identified 15 lateral gene transfer events that have occurred in this collection of Penicillium isolates, which might have played an important role, such as niche adaption, in the evolution of these fungi. The comprehensive characterization of the genomic diversity in the Penicillium genus supersedes single-reference genomes, which do not necessarily capture the entire genetic variation.https://doi.org/10.1186/s43008-023-00108-7Long read sequencingMinIONFilamentous fungiPenicilliumPhylogeneticsPangenome |
| spellingShingle | Celine Petersen Trine Sørensen Mikkel R. Nielsen Teis E. Sondergaard Jens L. Sørensen David A. Fitzpatrick Jens C. Frisvad Kåre L. Nielsen Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events IMA Fungus Long read sequencing MinION Filamentous fungi Penicillium Phylogenetics Pangenome |
| title | Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events |
| title_full | Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events |
| title_fullStr | Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events |
| title_full_unstemmed | Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events |
| title_short | Comparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events |
| title_sort | comparative genomic study of the penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events |
| topic | Long read sequencing MinION Filamentous fungi Penicillium Phylogenetics Pangenome |
| url | https://doi.org/10.1186/s43008-023-00108-7 |
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