Major transitions made easy? In search of genetic preconditions that help the repeated evolution and loss of fungal multicellularity

Projektinformationen

CONVERGENCE

ID Finanzhilfevereinbarung: 101086900

DOI

10.3030/101086900

EK-Unterschriftsdatum 11 Mai 2023

Startdatum 1 Juli 2023

Enddatum 30 Juni 2028

Finanziert unter

• European Research Council (ERC)

Gesamtkosten

€ 1 997 688,00

EU-Beitrag

€ 1 997 688,00

Koordiniert durch

HUN-REN Szegedi Biologiai Kutatokozpont
Hungary

Periodic Reporting for period 1 - CONVERGENCE (Major transitions made easy? In search of genetic preconditions that help the repeated evolution and loss of fungal multicellularity)

Berichtszeitraum: 2023-07-01 bis 2025-12-31

Zusammenfassung vom Kontext und den Gesamtzielen des Projekts

In this project we set out to study the genetic mechanisms of convergent evolution, by uncovering the mechanistic details of two highly replicated transitions in cellularity level. Convergent evolution is widespread in nature, even at macroevolutionary time scales. To explain its pervasive occurrence, recent studies have put forth the idea of predisposing precursor traits that, if easily co- or exapted for new functions, can increase the likelihood of convergence. However, most such hypotheses remain untested due to the lack of model systems that are tractable in the laboratory. We here identified two fungal case studies that offer optimal model systems to mechanistically test the hypothesis that predisposing traits increase the likelihood of convergence: (i) the 8-11 repeated origins of complex multicellularity in mushrooms and (ii) >14 losses of multicellularity in yeast-like fungi. We hypothesize that both of these happened by the repeated exaptation of ancient morphogenetic programs and, in the case of yeasts, additionally, of mechanisms for bypassing multicellular growth. Our hypotheses imply that both complex multicellular and yeast-like lifestyles are only a few mutations away for any filamentous fungus, because precursor traits shorten the mutational path for evolution. We designed an experimental plan involving phylogeny-aware comparative -omics, reverse genetics and evo-devo, which, combined with our preliminary results, will provide a robust entry point into testing the role of predisposition in convergent evolution and will ultimately allow us to ‘replay the tape of major fungal transitions’ in the laboratory. We expect this project to contribute to uncovering the general principles of convergent evolution and to be one of the first to mechanistically prove that certain precursor traits can promote convergence.

Arbeit, die ab Beginn des Projekts bis zum Ende des durch den Bericht erfassten Berichtszeitraums geleistet wurde, und die wichtigsten bis dahin erzielten Ergebnisse

We started all activities outlined in the proposal and have made good progress with each parallel task of both subprojects. In brief, early, data collection activities (mostly genomics, transcriptomics) have been completed, the data was analyzed and scrutinized for candidate genes that make the foundations of specific reverse genetics experiments in both subprojects. As a result, we obtained promising candidates that allow testing the genetic predisposition hypothesis. In addition, the data we have generated allows a global, transcriptome-wide search for patterns that are expected only under the scenario of a latent homology/genetic predisposition underlying the evolution of yeast-like growth and complex multicellularity. Although we are still early in the project, work so far has resulted in three journal publications in top-tier journals (Cell Genomics, Current Biology, Frontiers in Fungal Biology).

Fortschritte, die über den aktuellen Stand der Technik hinausgehen und voraussichtliche potenzielle Auswirkungen (einschließlich der bis dato erzielten sozioökonomischen Auswirkungen und weiter gefassten gesellschaftlichen Auswirkungen des Projekts)

The project has already resulted in several technological improvements that take fungal functional genomics beyond the state-of-the-art. In Hegedus et al 2025 (Cell Genomics) we present a new, comprehensive annotation of the C. cinerea genome. This solves several problems pertinent to mushroom genomics currently, such as the high fragmentation of draft genome sequences, the absence of precise gene model definitions, that of UTR, intergenic region and polyadenylation site predictions, to name a few. In another line of research, we implemented droplet-based single cell transcriptomics for mushroom-forming fungi for the first time and analyzed cellular heterogeneity in vegetative mycelium samples. The adaptation of this technique to mushrooms opens the door for key developmental biology and evo-devo, as well as industrial questions to be addressed.
One of the early experiments has led to the identification of sporulation-related genes, based on which, we initiated a side-project for the generation of sporeless mushroom strains. Sporeless strains are in great demand in the field of crop mushroom production; our preliminary results and proof-of-concept experiments helped us secure funding for this work (ERC Proo -of-Concept grant, starting Nov. 2025), which will help us move forward towards the development of new industrial strains and their commercialization.