A bright idea for studying bioluminescence in fungi
From fireflies to jellyfish, nature is full of bioluminescent species that emit light as a means of communicating, hunting or evading predators. While this phenomenon is always fascinating, its use by fungi is particularly interesting. That’s because most bioluminescent fungal species belong to Mycena, a very diverse genus of small mushroom-forming fungi. “What’s unique is that the 78 different bioluminescent fungi in this group don’t seem to be closely related, which suggests a complex history of bioluminescence loss across the species,” explains Jorinde Nuytinck, a researcher at the Naturalis Biodiversity Center. The problem is that a lack of a solid phylogenetic framework, combined with the fact that the genus is extremely elusive, has made it nearly impossible to test this theory. That is until now. With the support of the EU-funded GLiMMer project, Nuytinck, together with her colleague Brigida Gallone, created the first genome-based and species-rich classification of Mycena. This research was undertaken with the support of the Marie Skłodowska-Curie Actions programme.
A big collection of small mushrooms
To start, the project put together a large collection of Mycena species. While the project’s sampling came primarily from fungarium specimens, it also included specimens collected from citizen scientists. To increase the geographical and ecological breadth of the sampling, the collection prioritised specimens originating from non-temperate regions. “It is important to avoid a sampling bias as we didn’t know whether Mycena was temperate or tropical in origin,” says Gallone, who served as the project’s principal researcher. Next, researchers extracted genomic DNA from all the samples. This process not only revealed that fungarium DNA from historical specimens is highly degraded and fragmented, it also allowed for the drafting of genome assemblies and annotations for 10 new Mycena specimens. “From this work we were able to conclude that the diversity of Mycena mushrooms goes far beyond the current known diversity,” adds Gallone.
Genome-scale data key to solving fungi’s evolutionary questions
Based on findings such as this, the project developed the first ‘museomics’ approach to generating genome-scale data using historical fungal specimens. The approach works using a custom set of probes called bait to capture and sequence the target regions for the entire collection of selected Mycena specimens. Using this approach, the project assembled the first genome-based phylogenetic hypothesis for the Mycena genus. “Genome-scale data is very much needed to resolve key evolutionary questions in the fungal kingdom, and our museomics approach opens the door to exploring a treasure trove of fungaria,” remarks Gallone.
New insight into bioluminescence
When all the results are combined, researchers expect that its genome-based phylogenetic hypothesis will include more than 200 species. “This innovative phylogenomic framework will allow us to study the diversification of the bioluminescence cluster based on the presence or absence of its key components across a large set of species,” notes Gallone. Researchers plan to continue using their museomics methodology to create a new and stable classification for the genus Mycena and other fungal groups. The results achieved during the GLiMMer project will also form the basis for future project ideas and collaborations focused on a wider range of fungal diversity. “Despite the highly fundamental nature of this project, we provided methods that unlock a vast natural diversity that can be used to decipher evolution, characterise new biosynthetic pathways, and redefine species assignments in a genus that needs urgent prioritisation in conservation,” concludes Gallone.
Keywords
GLiMMer, bioluminescence, fungi, bioluminescent, Mycena, mushrooms, citizen scientists, genome-scale data
