Abstract: Global fungal biodiversity faces increasing conservation pressure, yet genome evolution in threatened fungal lineages remains poorly characterized. Here, we compared 28 fungal genomes spanning endangered and non-endangered lineages and contrasting trophic modes to examine variation in genome architecture, transposable elements, gene-family evolution, stress-related loci and secretome composition. Endangered fungi showed heterogeneous genome sizes and repeat landscapes, and no single genome-architecture pattern characterized all sampled endangered taxa. Gene-family turnover was predominantly lineage specific. After multiple-testing correction, no orthogroup was significantly expanded or contracted in all three focal endangered ectomycorrhizal fungi. An exploratory analysis of directional concordance nevertheless identified 9 orthogroups with concordant inferred expansion and 23 with concordant inferred contraction. Within the latter set, K13993 (HSP20; HSP20 family protein) was the only identical gene-level KEGG annotation recovered in all three focal species and was therefore examined as an exploratory candidate. Retained Hsp20-annotated coding sequences showed strong evolutionary constraint, whereas copy-number, promoter and transposable-element-neighbourhood patterns varied among species. Secretome and carbohydrate-active enzyme repertoires of the focal endangered ectomycorrhizal fungi largely overlapped those of other ectomycorrhizal fungi. These results do not support a universal genomic signature of fungal endangerment, but instead highlight substantial lineage dependence and provide a hypothesis-generating framework for future population-level and functional studies.

Key words: Comparative genomics, Ectomycorrhizal fungi, Transposable elements, Hsp20, Endangered fungi