A transcriptomic atlas of conserved responses in mushroom-forming fungi during interaction with competitors

Mushroom-forming fungi employ various protective strategies against competing organisms in their environment. Although considerable data exists on individual mushroom-forming fungi during interactions with other organisms, the extent to which defence mechanisms are conserved across Agaricomycetes is less known. In this study, we developed a comparative transcriptomic atlas to explore conserved transcriptional responses of the mushroom-forming fungi Schizophyllum commune, Coprinopsis cinerea, Agaricus bisporus, Pleurotus ostreatus, Lentinula edodes, and Flammulina velutipes during interaction with fungal, bacterial, and animal competitors. We performed a transcriptomic analysis on P. ostreatus and S. commune during interaction with the fungal mycoparasite Trichoderma harzianum, and we reanalysed nine previously published transcriptomics datasets. We identified 708 gene families containing genes that were up-regulated during interaction in at least three of the six mushroom-forming fungi. The transcriptional regulation of gene families involved in transport, small secreted proteins, redox activity, detoxification processes, and general stress responses were particularly conserved, suggesting their importance during fungal interactions. There is considerable overlap in the response to interaction with bacteria and fungi, and to a lesser extent with animals. This study provides a detailed mapping of shared transcriptomic responses in mushroom-forming fungi during interaction, offering new insights on how these fungi defend themselves during diverse microbial interactions.