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HEIndividual fellowship2022–2024

GLiMMer · Genomics of Luminescence in Mycena Mushrooms

Horizon Europe — Marie Skłodowska-Curie Actions

Duration
2022-08-01 → 2024-07-31
EU contribution
€203,464
Participants
1
Scheme
HORIZON-TMA-MSCA-PF-EF

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Results in brief

Genomics of Luminescence in Mycena Mushrooms

Bioluminescence, the emission of light by living organisms, is a fascinating phenomenon that evolved independently multiple times across the tree of life. It has been associated to a variety of ecological functions such as courtships, communication, luring prey and repulsing predators. In Fungi, bioluminescence has a single, de novo origin, and the majority of known bioluminescent fungal species (68/ca. 81) belongs to Mycena, a large and hyperdiverse genus of small mushroom-forming fungi in the Agaricales order (Basidiomycota). The genus counts ca. 1300 described species (names in https://www.indexfungorum.org/ 2023) and the non-bioluminescent members do not seem to form a monophyletic group. This implies a complex history of bioluminescence loss across Mycena species, potentially involving convergent and lineage-specific mechanisms. However, Mycena lacks a solid phylogenetic framework to test this hypothesis and due to its elusive nature, it remains one of the most under sampled fungal genera. In Fungi genes involved in the bioluminescent form a cluster (Bioluminescence gene cluster – BGC) composed by 4 known core genes plus a variable number of accessory and uncharacterized genes. Extensive rearrangements of the genes within the BGC and relocation of the cluster itself have been observed along the diversification of Mycena and its sister marasmioid clade, that includes Armillaria and Omphalotus species. Knowing the genomic context of the BCG across several species, might reveal the evolutionary circumstances of its diversification and loss and provide new clues on the interplay between lifestyle and genome architecture in fungi. The absence of a robust and densely sampled phylogenetic framework for the Mycena genus, together with the scarcity of chromosomal-level assemblies, impedes the reconstruction of the evolutionary history that led to the birth and death of the fungal bioluminescence gene cluster. The goal of this project is to generate the first, genome-based, and species-rich classification of Mycena that integrates present-day and historical (type-)specimens from museum collections.

Data: CORDIS, © European Union

Project objective

Sailors called it burning of the sea, Shakespeare described it as pale fire and Aristotle named it cold light. The glimmer they witnessed was light emitted by living organisms or bioluminescence. While it represents one of the most striking examples of convergent evolution across the tree of life, in Fungi it has a single origin in the Agaricales order, Basidiomycota. In particular, Mycena, a large genus of mushroom-forming fungi, includes most of known bioluminescent species together with hundreds of species that lost the ability to emit light. In GLiMMer, I will study the evolution of fungal bioluminescence and test the hypothesis that multiple, lineage-specific mechanisms led to the convergent loss of this trait, providing clues for its ecological relevance. To date, Mycena lacks a robust phylogenetic framework and is heavily under sampled. Fungarium collections, such as the one at Naturalis, preserved thousands of Mycena specimens over the past centuries. Thanks to new high-throughput sequencing methods these collections are being transformed in genomics resources, bridging taxonomy and evolution. In GLiMMer, my expertise in fungal genomics will serve to develop a genome-based classification of Mycena, that combines contemporary and museum specimens. I will generate assemblies of 100 representative species using short-read sequencing. Next, I will extract phylogenetically informative loci to design a target sequence capture method for recalcitrant museum specimens for the first time in mushrooms. Then, I will use the new classification to select reference species and obtain chromosomal-level assemblies using long-read sequencing. Finally, with genome-wide synteny analyses I will investigate the evolutionary circumstances that led to the birth and death of bioluminescence in Fungi. By integrating taxonomy, genomics and evolution, my project will create a paradigm shift in our knowledge on fungal biodiversity and ultimately contribute to its conservation.

Original text from CORDIS.

Participants

  • STICHTING NATURALIS BIODIVERSITY CENTER · LeidenCoordinatorNetherlands

Links

Data: CORDIS, © European Union