Comparative genomics of Aspergillus nidulans and section Nidulantes
Aspergillus nidulans is an important model organism for eukaryotic biology and the reference for the section Nidulantes in comparative studies. In this study, we de novo sequenced the genomes of 25 species of this section. Whole-genome phylogeny of 34 Aspergillus species and Penicillium chrysogenum...
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2025-01-01
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| Series: | Current Research in Microbial Sciences |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666517425000045 |
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| author | Sebastian Theobald Tammi Vesth Jane L. Nybo Jens C. Frisvad Inge Kjærbølling Stephen Mondo Kurt LaButti Sajeet Haridas Robert Riley Alan A. Kuo Asaf A. Salamov Jasmyn Pangilinan Anna Lipzen Maxim Koriabine Mi Yan Kerrie Barry Alicia Clum Ellen K. Lyhne Elodie Drula Ad Wiebenga Astrid Müller Ronnie J.M. Lubbers Roland S. Kun Ana Carolina dos Santos Gomes Miia R. Mäkelä Bernard Henrissat Blake A. Simmons Jon K. Magnuson Jakob B. Hoof Uffe H. Mortensen Paul S. Dyer Michelle Momany Thomas O. Larsen Igor V Grigoriev Scott E. Baker Ronald P. de Vries Mikael R. Andersen |
| author_facet | Sebastian Theobald Tammi Vesth Jane L. Nybo Jens C. Frisvad Inge Kjærbølling Stephen Mondo Kurt LaButti Sajeet Haridas Robert Riley Alan A. Kuo Asaf A. Salamov Jasmyn Pangilinan Anna Lipzen Maxim Koriabine Mi Yan Kerrie Barry Alicia Clum Ellen K. Lyhne Elodie Drula Ad Wiebenga Astrid Müller Ronnie J.M. Lubbers Roland S. Kun Ana Carolina dos Santos Gomes Miia R. Mäkelä Bernard Henrissat Blake A. Simmons Jon K. Magnuson Jakob B. Hoof Uffe H. Mortensen Paul S. Dyer Michelle Momany Thomas O. Larsen Igor V Grigoriev Scott E. Baker Ronald P. de Vries Mikael R. Andersen |
| author_sort | Sebastian Theobald |
| collection | DOAJ |
| description | Aspergillus nidulans is an important model organism for eukaryotic biology and the reference for the section Nidulantes in comparative studies. In this study, we de novo sequenced the genomes of 25 species of this section. Whole-genome phylogeny of 34 Aspergillus species and Penicillium chrysogenum clarifies the position of clades inside section Nidulantes. Comparative genomics reveals a high genetic diversity between species with 684 up to 2433 unique protein families. Furthermore, we categorized 2118 secondary metabolite gene clusters (SMGC) into 603 families across Aspergilli, with at least 40 % of the families shared between Nidulantes species. Genetic dereplication of SMGC and subsequent synteny analysis provides evidence for horizontal gene transfer of a SMGC. Proteins that have been investigated in A. nidulans as well as its SMGC families are generally present in the section Nidulantes, supporting its role as model organism. The set of genes encoding plant biomass-related CAZymes is highly conserved in section Nidulantes, while there is remarkable diversity of organization of MAT-loci both within and between the different clades. This study provides a deeper understanding of the genomic conservation and diversity of this section and supports the position of A. nidulans as a reference species for cell biology. |
| format | Article |
| id | doaj-art-08c1d05a8154446ba1779a8af0da9892 |
| institution | Kabale University |
| issn | 2666-5174 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
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| series | Current Research in Microbial Sciences |
| spelling | doaj-art-08c1d05a8154446ba1779a8af0da98922025-01-20T04:17:56ZengElsevierCurrent Research in Microbial Sciences2666-51742025-01-018100342Comparative genomics of Aspergillus nidulans and section NidulantesSebastian Theobald0Tammi Vesth1Jane L. Nybo2Jens C. Frisvad3Inge Kjærbølling4Stephen Mondo5Kurt LaButti6Sajeet Haridas7Robert Riley8Alan A. Kuo9Asaf A. Salamov10Jasmyn Pangilinan11Anna Lipzen12Maxim Koriabine13Mi Yan14Kerrie Barry15Alicia Clum16Ellen K. Lyhne17Elodie Drula18Ad Wiebenga19Astrid Müller20Ronnie J.M. Lubbers21Roland S. Kun22Ana Carolina dos Santos Gomes23Miia R. Mäkelä24Bernard Henrissat25Blake A. Simmons26Jon K. Magnuson27Jakob B. Hoof28Uffe H. Mortensen29Paul S. Dyer30Michelle Momany31Thomas O. Larsen32Igor V Grigoriev33Scott E. Baker34Ronald P. de Vries35Mikael R. Andersen36Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, DenmarkDepartment of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, DenmarkDepartment of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, DenmarkDepartment of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, DenmarkDepartment of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, DenmarkDepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USADepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USADepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USADepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USADepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USADepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USADepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USADepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USADepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USADepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USADepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USADepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USADepartment of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, DenmarkArchitecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France; Biodiversité et Biotechnologie Fongiques, UMR 1163, INRAE, Marseille, FranceFungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The NetherlandsFungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The NetherlandsFungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The NetherlandsFungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The NetherlandsFungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The NetherlandsDepartment of Microbiology, University of Helsinki, FinlandDepartment of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, DenmarkUS Department of Energy Joint Bioenergy Institute, Berkeley, CA, USAUS Department of Energy Joint Bioenergy Institute, Berkeley, CA, USADepartment of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, DenmarkDepartment of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, DenmarkSchool of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UKFungal Biology Group & Plant Biology Department, University of Georgia, Athens, Georgia, USA 30602Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, DenmarkDepartment of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USASchool of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, USA; Corresponding authors.Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; Corresponding authors.Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; Corresponding authors.Aspergillus nidulans is an important model organism for eukaryotic biology and the reference for the section Nidulantes in comparative studies. In this study, we de novo sequenced the genomes of 25 species of this section. Whole-genome phylogeny of 34 Aspergillus species and Penicillium chrysogenum clarifies the position of clades inside section Nidulantes. Comparative genomics reveals a high genetic diversity between species with 684 up to 2433 unique protein families. Furthermore, we categorized 2118 secondary metabolite gene clusters (SMGC) into 603 families across Aspergilli, with at least 40 % of the families shared between Nidulantes species. Genetic dereplication of SMGC and subsequent synteny analysis provides evidence for horizontal gene transfer of a SMGC. Proteins that have been investigated in A. nidulans as well as its SMGC families are generally present in the section Nidulantes, supporting its role as model organism. The set of genes encoding plant biomass-related CAZymes is highly conserved in section Nidulantes, while there is remarkable diversity of organization of MAT-loci both within and between the different clades. This study provides a deeper understanding of the genomic conservation and diversity of this section and supports the position of A. nidulans as a reference species for cell biology.http://www.sciencedirect.com/science/article/pii/S2666517425000045AspergillusComparative genomicsNidulantesSecondary metabolismCAZy |
| spellingShingle | Sebastian Theobald Tammi Vesth Jane L. Nybo Jens C. Frisvad Inge Kjærbølling Stephen Mondo Kurt LaButti Sajeet Haridas Robert Riley Alan A. Kuo Asaf A. Salamov Jasmyn Pangilinan Anna Lipzen Maxim Koriabine Mi Yan Kerrie Barry Alicia Clum Ellen K. Lyhne Elodie Drula Ad Wiebenga Astrid Müller Ronnie J.M. Lubbers Roland S. Kun Ana Carolina dos Santos Gomes Miia R. Mäkelä Bernard Henrissat Blake A. Simmons Jon K. Magnuson Jakob B. Hoof Uffe H. Mortensen Paul S. Dyer Michelle Momany Thomas O. Larsen Igor V Grigoriev Scott E. Baker Ronald P. de Vries Mikael R. Andersen Comparative genomics of Aspergillus nidulans and section Nidulantes Current Research in Microbial Sciences Aspergillus Comparative genomics Nidulantes Secondary metabolism CAZy |
| title | Comparative genomics of Aspergillus nidulans and section Nidulantes |
| title_full | Comparative genomics of Aspergillus nidulans and section Nidulantes |
| title_fullStr | Comparative genomics of Aspergillus nidulans and section Nidulantes |
| title_full_unstemmed | Comparative genomics of Aspergillus nidulans and section Nidulantes |
| title_short | Comparative genomics of Aspergillus nidulans and section Nidulantes |
| title_sort | comparative genomics of aspergillus nidulans and section nidulantes |
| topic | Aspergillus Comparative genomics Nidulantes Secondary metabolism CAZy |
| url | http://www.sciencedirect.com/science/article/pii/S2666517425000045 |
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