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

Summary

Researchers created a detailed genetic instruction manual for a common mushroom species called Coprinopsis cinerea. Using advanced sequencing technology, they identified all the genes and precisely mapped where genes start and stop, what controls them, and how they respond to light and hunger. This improved genetic map reveals how mushrooms form fruiting bodies and survive changing environmental conditions, providing a valuable resource for understanding mushroom biology and improving mushroom cultivation.

Background

Mushroom-forming fungi (Agaricomycetes) are important for biotechnology and lignocellulosic biomass degradation, but their genomes lack high-quality annotations and functional information. Coprinopsis cinerea is a key model organism for studying mushroom development, yet comprehensive genomic resources with detailed gene annotations are limited.

Objective

To create a comprehensively annotated genome for C. cinerea by integrating a new chromosome-level assembly with long-read sequencing data and extensive gene expression profiling across multiple developmental and environmental conditions.

Results

The new annotation includes 13,617 genes with 14,750 transcripts, comprehensive UTR annotations for 88-89% of genes, identification of 1,165 genes with microexons, and detection of 76,879 polyadenylation site clusters. Core gene sets were identified for carbon starvation response (1,759 genes), light response (2,340 genes), and mycelial differentiation with insights into early and late light-induced genes.

Conclusion

C. cinerea now has the most comprehensively annotated genome among mushroom-forming fungi, providing critical functional insights into starvation, light responses, and multicellular development. The annotated resources are publicly available and will support research on fungal development, stress responses, and biotechnology applications.
  • Published in:Cell Genomics,
  • Study Type:Genomics and Transcriptomics Study,
  • Source: PMID: 40262612, DOI: 10.1016/j.xgen.2025.100853
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