Morphogenesis, starvation, and light responses in a mushroom-forming fungus revealed by long-read sequencing and extensive expression profiling

Hegedüs, Botond and Sahu, Neha and Bálint, Balázs and Haridas, Sajeet and Bense, Viktória and Merényi, Zsolt and Virágh, Máté and WU, HONGLI and Liu, Xiao-Bin and Riley, Robert and Lipzen, Anna and Koriabine, Maxim and Savage, Emily and Guo, Jie and Barry, Kerrie and Ng, Vivian and Urbán, Péter and Gyenesei, Attila and Freitag, Michael and Grigoriev, Igor V and Nagy, László (2025) Morphogenesis, starvation, and light responses in a mushroom-forming fungus revealed by long-read sequencing and extensive expression profiling. CELL GENOMICS, 5 (6). No. 100853. ISSN 2666-979X

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Abstract

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.

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