Comparative genomics of Aspergillus nidulans and section Nidulantes
| Title: | Comparative genomics of Aspergillus nidulans and section Nidulantes |
|---|---|
| Authors: | Theobald, Sebastian; Vesth, Tammi; Nybo, Jane L.; Frisvad, Jens C.; Kjærbølling, Inge; Mondo, Stephen; LaButti, Kurt; Haridas, Sajeet; Riley, Robert; Kuo, Alan A.; Salamov, Asaf A.; Pangilinan, Jasmyn; Lipzen, Anna; Koriabine, Maxim; Yan, Mi; Barry, Kerrie; Clum, Alicia; Lyhne, Ellen K.; Drula, Elodie; Wiebenga, Ad; Müller, Astrid; Lubbers, Ronnie J.M.; Kun, Roland S.; dos Santos Gomes, Ana Carolina; Mäkelä, Miia R.; Henrissat, Bernard; Simmons, Blake A.; Magnuson, Jon K.; Hoof, Jakob B.; Mortensen, Uffe H.; Dyer, Paul S.; Momany, Michelle; Larsen, Thomas O.; Grigoriev, Igor V.; Baker, Scott E.; de Vries, Ronald P.; Andersen, Mikael R. |
| Contributors: | Helsinki Institute of Sustainability Science (HELSUS); Fungal Genetics and Biotechnology; Department of Microbiology |
| Publisher Information: | Elsevier B.V. |
| Publication Year: | 2025 |
| Collection: | Helsingfors Universitet: HELDA – Helsingin yliopiston digitaalinen arkisto |
| Subject Terms: | Aspergillus; CAZy; Comparative genomics; Nidulantes; Secondary metabolism; 11832 Microbiology and virology |
| 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. ; Peer reviewed |
| Document Type: | article in journal/newspaper |
| File Description: | application/pdf |
| Language: | English |
| Relation: | The work (proposal 10.46936/10.25585/60001025) performed at the US Department of Energy (DOE) Joint BioEnergy Institute and the US DOE Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the US DOE. MRM acknowledges funding from Research Council of Finland (grant no. 314102) and Novo Nordisk Foundation (grant no. NNF21OC0067087) . MRA, IK, JLN, ST and TCV gratefully acknowledge funding from the Villum Foundation, Grant VKR023437. MRA, IK and TCV acknowledge funding from the Danish National Research Foundation, grant number DNRF137. MRA acknowledges support from the Jorck Foundation. PSD thanks the Wellcome Trust (UK) for funding (no. 219551/Z/19/Z).; Theobald, S, Vesth, T, Nybo, J L, Frisvad, J C, Kjærbølling, I, Mondo, S, LaButti, K, Haridas, S, Riley, R, Kuo, A A, Salamov, A A, Pangilinan, J, Lipzen, A, Koriabine, M, Yan, M, Barry, K, Clum, A, Lyhne, E K, Drula, E, Wiebenga, A, Müller, A, Lubbers, R J M, Kun, R S, dos Santos Gomes, A C, Mäkelä, M R, Henrissat, B, Simmons, B A, Magnuson, J K, Hoof, J B, Mortensen, U H, Dyer, P S, Momany, M, Larsen, T O, Grigoriev, I V, Baker, S E, de Vries, R P & Andersen, M R 2025, 'Comparative genomics of Aspergillus nidulans and section Nidulantes', Current Research in Microbial Sciences, vol. 8, 100342. https://doi.org/10.1016/j.crmicr.2025.100342; https://hdl.handle.net/10138/590904; 85215107170; 001404906200001 |
| Availability: | https://hdl.handle.net/10138/590904 |
| Rights: | cc_by ; info:eu-repo/semantics/openAccess ; openAccess |
| Accession Number: | edsbas.3F89A1F9 |
| Database: | BASE |