Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range

Authors: Drott, Milton; CHUL PARK, SUNG - University Of Wisconsin; WEN WANG, YEN - University Of Wisconsin; HARROW, LYNN - University Of Wisconsin; KELLER, NANCY - University Of Wisconsin; PRINGLE, ANN - University Of Wisconsin

Submitted to: The ISME Journal: Multidisciplinary Journal of Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/4/2023
Publication Date: 5/23/2023
Citation: Drott, M.T., Chul Park, S., Wang, Y., Harrow, L., Keller, N.P., Pringle, A. 2023. Pangenomics of the death cap mushroom Amanita phalloides, and of Agaricales, reveals dynamic evolution of toxin genes in an invasive range. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. https://doi.org/10.1038/s41396-023-01432-x.
DOI: https://doi.org/10.1038/s41396-023-01432-x

Interpretive Summary: The 'death cap' is the most deadly mushroom. While this fungus is native to Europe, it is invasive to the west coast of the United States (US). Deadly poisonings associated with this mushroom have raised serious concerns about the continued eastward spread of this fungus in the US. A small number of toxins that have been purified from these mushrooms have proven extremely valuable to the biomedical industry and as pharmaceuticals. Despite the notoriety of this organism and the potential uses of the few known toxins, very little is known about the overall extent of toxin diversity in this species. In this study we developed new computational tools that allow for large-scale identification of toxin-related genes from genome sequence data. Comparing genomes of mushrooms from Europe and the US, we identify eight previously-unknown toxin genes. We show that the diversity of toxin genes is different in the native and invasive range of this fungus and suggest that these differences may be associated with the introduction of this fungus and subsequent spread. Our work unlocks a new trove of toxins for drug-discovery while also pointing to factors that may help explain the invasive success of this fungus and may ultimately help us control it's spread.

Technical Abstract: The deadly-poisonous Amanita phalloides is invading California but the role of toxic secondary metabolites in the invasion is unknown. We developed a bioinformatic pipeline to automate identification of toxin-associated MSDIN genes and probed 88 genomes from California and the native European range, discovering a diverse MSDIN pangenome with both core and accessory elements. Toxin genes are maintained by strong natural selection. Genes are clustered within genomes. MSDIN diversity was generated by ancient and independent gene-family expansions among genera of Agaricales. We report the discovery of an MSDIN in an Amanita outside the clade of "lethal Amanitas". The dynamic evolution of the Agaricales-MSDIN pangenome underscores the potential role of these compound’s in mediating ecological interactions in A. phalloides' ranges and is reshaping our understanding of the genes' evolutionary history. Our results enable drug-prospecting efforts in a previously-inaccessible class of compound, providing a roadmap to approach metabolites found in Basidiomycete genomes.