Abstract
Tricholoma matsutake, a highly valued ectomycorrhizal fungus, requires a symbiotic relationship with pine trees for growth, complicating its cultivation. This study presents a comprehensive comparative genomic analysis of Tricholoma species, with a focus on T. matsutake. Genomic data from 19 assemblies representing 13 species were analyzed to identify genus-, species-, and strain-specific genes, revealing significant evolutionary adaptations. Notably, T. matsutake exhibits a higher proportion of repetitive elements compared to other species, with retrotransposons like LTR Gypsy dominating its genome. Phylogenomic analyses showed that T. matsutake forms a monophyletic group closely related to T. bakamatsutake. Gene family expansion and contraction analyses highlighted the unique evolutionary pressures on T. matsutake, particularly the loss of tryptophan-related metabolic pathways and the gain of genes related to iron ion homeostasis, which may be crucial for its adaptation to nutrient-limited environments. Additionally, the reduction in secreted proteins and carbohydrate-active enzymes reflects the host-dependent lifestyle of T. matsutake and related species. These findings enhance our understanding of the genetic and evolutionary mechanisms underlying the complex symbiotic relationships of T. matsutake, offering potential avenues for optimizing its cultivation and commercial value.