Current Research in Microbial Sciences (Jan 2025)
Comparative genomics of Aspergillus nidulans and section Nidulantes
- 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
Affiliations
- Sebastian Theobald
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Tammi Vesth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Jane L. Nybo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Inge Kjærbølling
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Stephen Mondo
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Kurt LaButti
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Sajeet Haridas
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Robert Riley
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Alan A. Kuo
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Asaf A. Salamov
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Jasmyn Pangilinan
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Maxim Koriabine
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Mi Yan
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Alicia Clum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Ellen K. Lyhne
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France; Biodiversité et Biotechnologie Fongiques, UMR 1163, INRAE, Marseille, France
- Ad Wiebenga
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Astrid Müller
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Ronnie J.M. Lubbers
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Roland S. Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Ana Carolina dos Santos Gomes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Miia R. Mäkelä
- Department of Microbiology, University of Helsinki, Finland
- Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Blake A. Simmons
- US Department of Energy Joint Bioenergy Institute, Berkeley, CA, USA
- Jon K. Magnuson
- US Department of Energy Joint Bioenergy Institute, Berkeley, CA, USA
- Jakob B. Hoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Uffe H. Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Paul S. Dyer
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK
- Michelle Momany
- Fungal Biology Group & Plant Biology Department, University of Georgia, Athens, Georgia, USA 30602
- Thomas O. Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- Igor V Grigoriev
- Department 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, USA
- Scott E. Baker
- School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, USA; Corresponding authors.
- Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; Corresponding authors.
- Mikael R. Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; Corresponding authors.
- Journal volume & issue
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Vol. 8
p. 100342
Abstract
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.
