Morphogenesis, starvation, and light responses in a mushroom-forming fungus revealed by long-read sequencing and extensive expression profiling
Mushroom-forming fungi (Agaricomycetes) are emerging as pivotal players in several fields of science and industry. Genomic data for Agaricomycetes are accumulating rapidly; however, this is not paralleled by improvements of gene annotations, which leave gene function notoriously poorly understood. We set out to improve our functional understanding of the model mushroom Coprinopsis cinerea by integrating a new, chromosome-level assembly, high-quality gene predictions, and functional information derived from broad gene-expression profiling data. The new annotation includes 5' and 3' untranslated regions (UTRs), polyadenylation sites (PASs), upstream open reading frames (uORFs), splicing isoforms, and microexons, as well as core gene sets corresponding to carbon starvation, light response, and hyphal differentiation. As a result, the genome of C. cinerea has now become the most comprehensively annotated genome among mushroom-forming fungi, which will contribute to multiple rapidly expanding fields, including research on their life history, light and stress responses, as well as multicellular development.
Authors
- Vivian Ng (ORCID: https://orcid.org/0000-0001-8941-6931)
- Igor V. Grigoriev (ORCID: https://orcid.org/0000-0002-3136-8903)
- Attila Gyenesei (ORCID: https://orcid.org/0000-0003-2925-9342)
- Kerrie Barry (ORCID: https://orcid.org/0000-0002-8999-6785)
- László G. Nagy (ORCID: https://orcid.org/0000-0002-4102-8566)
- Viktória Bense
- Emily Savage (ORCID: https://orcid.org/0000-0002-7129-8989)
- Sajeet Haridas (ORCID: https://orcid.org/0000-0002-0229-0975)
- Anna Lipzen (ORCID: https://orcid.org/0000-0003-2293-9329)
- Balázs Bálint (ORCID: https://orcid.org/0000-0002-5102-0787)
- Máté Virágh
- Péter Urbán (ORCID: https://orcid.org/0000-0003-4043-3428)
- Robert Riley (ORCID: https://orcid.org/0000-0003-0224-0975)
- Zsolt Merényi
- Michael Freitag (ORCID: https://orcid.org/0000-0003-1174-8252)
- Maxim Koriabine
- Jie Guo (ORCID: https://orcid.org/0000-0002-3731-288X)
- Hongli Wu (ORCID: https://orcid.org/0000-0001-6632-3118)
- Botond Hegedüs
- Xiaobin Liu (ORCID: https://orcid.org/0000-0001-7091-2660)
- Neha Sahu (ORCID: https://orcid.org/0009-0003-6737-7099)
Institutions
- Oregon State University (US)
- Lawrence Berkeley National Laboratory (US)
- Joint Genome Institute (US)
- University of Pecs (HU)
Publication Details
- Journal
- Cell Genomics
- Published
- 2025-04-21
- DOI
- https://doi.org/10.1016/j.xgen.2025.100853
- Citations
- 3
- Primary Topic
- Fungal Biology and Applications
- Type
- article
- Field-Weighted Citation Impact
- 4.18