Comparative mitochondrial genomics of the medicinal mushroom Phellinus tuberculosus reveals conserved core genes and dynamic genome evolution within Hymenochaetaceae

Phellinus species are well-known white-rot fungi belonging to the Hymenochaetaceae family. Phellinus species contain medicinally functional compounds and nutrients. However, a comprehensive genus-level analysis of their mitochondrial genomes remains unavailable to date. The complete mitochondrial genome of P. tuberculosus (115,079 bp, 26.1% GC) was assembled, annotated, and analyzed based on comparative genomic analysis with two previously available Phellinus species. Fourteen core protein-coding genes, 27 tRNA genes, and 2 rRNA genes were annotated, along with 79 simple sequence repeats and multiple repeat sequences. A total of 42 RNA C-to-U editing sites were predicted, with nad 2 exhibiting the highest number of editing sites. Comparative genomic and phylogenomic analyses showed that the P. tuberculosus lineage shared conserved mitochondrial genome features and clustered with the two previously characterized Phellinus species in a strongly supported clade. This study conducts a comprehensive analysis of Phellinus mitochondrial genomes and describes the first complete mitochondrial genome of P. tuberculosus . The findings illustrate the evolutionary conservation of mitochondrial genomes within Phellinus , advance the current understanding of fungal evolution and the potential medicinal use of fungi, and provide a valuable genomic resource for phylogenetic, ecological, and biotechnological studies of medicinally important species.