Using a whole-genome-based comparison with free-living members of the genus Xylaria, we document that the association has been accompanied by significant reductions in genome size, protein-coding gene content, and reduced functional capacities related to oxidative lignin degradation, oxidative stress responses and secondary metabolite production. Capitalizing on viable Pseudoxylaria cultures from different termite colonies, we obtained genomes of seven and transcriptomes of two Pseudoxylaria isolates. Insights into the genomic and metabolic consequences of their association, however, have remained sparse. Pseudoxylaria are inconspicuously present in active fungus gardens of termite colonies and only emerge in the form of vegetative stromata, when the fungus comb is no longer attended (“sit and wait” strategy). In this study, we investigated a distinct subgeneric taxon of Xylaria ( Xylariaceae), named Pseudoxylaria, whose members have solely been isolated from the fungus garden of farming termites. Characterizing ancient clades of fungal symbionts is necessary for understanding the evolutionary process underlying symbiosis development.

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