Fungal Code Cracked: Scientists Map Mushroom Gene Activity in Response to Light, Hunger, and Growth

In a remarkable leap for fungal genetics, researchers have created the most detailed gene map to date of a mushroom-forming fungus, shedding light—literally—on how mushrooms grow, adapt, and respond to their environment. The study, published in Cell Genomics, unveils a high-resolution transcriptome of the mushroom Coprinopsis cinerea, a model fungus, using state-of-the-art long-read sequencing and multi-condition expression profiling.

Why does it matter? Because mushrooms aren’t just for food—they’re a goldmine for bioengineering, medicine, and sustainable technologies. And now, scientists finally have the blueprint to hack their biology.

What’s New?

The international team, led by Hungarian and U.S. researchers, assembled a chromosome-level genome for C. cinerea and profiled its genetic activity under 67 different conditions, including carbon starvation, light exposure, and developmental transitions such as aerial versus submerged mycelium.

The study produced:

A near-complete, manually curated genome annotation
13,617 gene models with improved accuracy
Full-length annotations of untranslated regions (UTRs), microexons, and polyadenylation sites
The most robust analysis to date of genes involved in mushroom morphogenesis, light response, and nutrient stress

Light and Hunger Trigger Mushroom Behavior

One of the most exciting discoveries is how environmental triggers—light and starvation—activate specific gene networks that prepare the fungus for reproduction.

In darkness:

The fungus expresses plant cell wall-degrading enzymes, scavenging for carbon.
It activates genes involved in autophagy and cell wall remodeling—possibly digesting itself to survive.

With light exposure:

Two waves of gene activation occur:
- An early wave (1–6 hours) tied to DNA repair and blue-light sensors
- A late wave (12–24 hours) tied to cell wall biosynthesis, membrane dynamics, and fruiting body formation

Notably, the study identified over 2,300 light-responsive genes and 1,700 starvation-responsive genes, many of which overlap with developmental processes.

Why This Mushroom?

C. cinerea is a superstar in fungal biology—fast-growing, genetically tractable, and capable of forming complex fruiting bodies. But until now, even its genome lacked high-quality annotations, limiting its utility for molecular studies.

With this new data, C. cinerea is now the most comprehensively annotated mushroom species, surpassing other Agaricomycetes in genomic precision.

Key Technical Breakthroughs

Long-read sequencing (ONT + PacBio) allowed the detection of alternative transcripts, uORFs, and microexons.
QuantSeq 3′ end sequencing revealed patterns of alternative polyadenylation, showing that most genes prefer one short, dominant transcript variant.
The researchers also built a public database—MushroomDB—allowing scientists worldwide to explore gene expression in mushrooms under various conditions.

Future Implications

This high-resolution mushroom transcriptome opens the door to:

Synthetic biology applications using fungal chassis organisms
Engineering mushrooms for biodegradation, drug production, or climate-resilient agriculture
Discovering light-responsive gene circuits for optogenetics or photobioreactors
Better understanding of fungal multicellularity and development, comparable to what yeast has done for molecular biology

Bottom Line

The fungus may live in the dark, but its genome is now fully in the light.

With this landmark study, mushrooms are no longer mysterious forest dwellers—they’re emerging as programmable, sustainable biofactories, guided by a high-resolution genetic roadmap.

Reference

Hegedüs, B., Sahu, N., Bálint, B., Haridas, S., Bense, V., Merényi, Z., … & Nagy, L. G. (2025). Morphogenesis, starvation, and light responses in a mushroom-forming fungus revealed by long-read sequencing and extensive expression profiling. Cell Genomics. https://doi.org/10.1016/j.xgen.2025.100853