Comparative mitochondrial genome analyses of five medicinal mushroom Sanghuangporus provide insights into conservation, variation, and phylogenetic relationships

Sanghuangporus species are white-rot basidiomycetes of notable ecological and economic importance, playing critical roles in wood decomposition and medicinal applications. However, comprehensive genus-level mitochondrial genome analyses for Sanghuangporus remain limited, which constrains understanding of mitochondrial genome evolution within this lineage. The second- and third-generation sequencing alongside comparative genomic approaches, we analyzed the mitochondrial genomes of five Sanghuangporus species (S. weigelae, S. lonicericola, S. alpinus, S. sanghuang, and S. vaninii). Genome sizes ranged from 97,345 to 116,792 bp, with GC contents between 23.21% and 24.04%. Comparative analyses revealed that mitochondrial genome expansion within the Hymenochaetaceae is primarily driven by intron gain. While core protein-coding genes (PCGs) have remained largely conserved, rearrangements were detected in intergenic regions, highlighting the dynamic structural evolution of these fungal mitochondrial genomes. Phylogenetic analyses based on concatenated PCGs and cox1 robustly resolved Sanghuangporus as a monophyletic clade. Among the conserved PCGs, atp9 and nad4L exhibited the lowest genetic divergence, all genes displayed Ka/Ks ratios < 1, indicating that they were under pervasive purifying selection. Repeat contents, nucleotide diversity, codon usage bias, tRNA secondary structures, and RNA-editing patterns were also characterized. This study provides the first genus-level comprehensive mitochondrial genomic framework for Sanghuangporus, illustrating how fungal mitochondrial genomes evolve through intron-mediated expansion, structural rearrangement, and strong functional constraint. Our findings broadly contribute to the understanding of mitochondrial genome evolution in fungi and provide a valuable resource for evolutionary, ecological, and biotechnological studies of medicinally important species.