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Comparative transcriptomics of the widespread Mycena mushrooms: What genomic features makes saprotrophs turn into opportunistic biotrophs and symbionts?

Internationalisation Fellowships


My project aims to discover the molecular mechanisms fungi use to switch between their different lifestyles, and how they adapt to extreme habitats such as the Arctic Tundra. Fungi perform notable ecosystem functions in nature, both beneficial - as degraders of dead material (saprotrophs) and in symbiotic relationships with vascular plants (mycorrhizal) - and harmful, as parasites on plants and animals (pathogens), or as degraders of houses/buildings. I use the genus Mycena as model organisms, since I have recently discovered that there are species shifting between these different life forms within this single genus, and since I have found Arctic species to have 10 times larger genomes than most fungi. I will be based at Lund University who are world-leading experts in genomics of fungi.


In many projects sequencing fungal genomes, the ecology (lifestyle) of the species analysed is being been taken for granted based on general assumptions of a whole genus. Here, we have already directly tested the growth of the fungi on different media and their interaction with host plants, and expand on this alongside our sequencing their genomics and transcriptomics (gene expression). Because of this, and since our study organisms are closely related, yet display a continuum of ecologies - saprotrophic, parasitic and beneficial - we are much better able to directly identify recently evolved features, the genetic mechanims that controls them, and how they work. This could elucidate enigmatic parts of the fungal evolution which are of direct interest to all scientists working with fungi.


My research will be done in collaboration with 5 institutions that all have specific expertise in each subfield I need. I will go to Greenland with Jacob Heilmann-Clausen (University of Copenhagen) to obtain Artic mycorrhiza-fungi for genome sequencing. Joint Genome Institute (USA) and University of Nancy(France) will assist the genome sequencing. I will grow my Mycena and Mhost plant(birch) cultures in Lund, extract the DNA/RNA there, and then analyse their gene expression in cooperation with Lund and The Oslo Mycology Group. Finally, I will take Mycena-infected birch roots to the Natural History Museum of Paris, where they specialise in the FISH-hybridisation technique, to identify Mycena species that assemble near the root tip and are likely to be mycorrhizal.


Fungi have a direct impact on the human economy. It has long been known that the (beneficial) mycorrhizal infection in host trees/crops increases their health and growth. Furthermore, about 60% of the thousands of commercial enzymes used in dairies, detergent production, paper mills, in brewing or in the biofuel industries are originally derived from fungi. Conversely, as much as 16% of all crop harvests globally are lost to pathogenic fungi, and dry rot wood-decaying fungi destroying buildings are known as a major problem to many homeowners around the world. Our genome sequencing and identification of fungal genes form a very direct basis from which the biotech industry may extract information about fungal enzymes which they can then later modify and optimise for their specific needs.