Mitogenome characterization and organellar genome evolution in achlorophyllous orchid Chamaegastrodia shikokiana Makino & F.Maek. (Orchidaceae).

BACKGROUND: While plastome evolution in mycoheterotrophic plants is well documented, the mitogenome remains poorly characterized in these lineages—particularly within Orchidaceae, where no complete mitogenomes from the subfamily Orchidoideae have been reported in Genbank. Here, we present the first complete mitogenome of Chamaegastrodia shikokiana, a fully mycoheterotrophic orchid in Orchidoideae, to investigate its mitogenomic structure, gene content, and intracellular gene transfers. RESULTS: The mitogenome of Chamaegastrodia shikokiana, consists of 19 contigs with a total length of 412,787 bp. Unlike its reduced plastome, the mitogenome retains almost the full complement of protein-coding genes except four genes (nad1 exon1, rpl2, rpl16, and rps19). Twenty-one plastome-derived homologous regions were detected in the mitogenome, including photosynthetic-related and housekeeping genes. Phylogenetic analysis of rbcL-like sequences indicated recurrent intracellular gene transfer events. Despite this, no clear correlation was found between transferred regions and elevated substitution rates or selection pressure. RELAX analysis revealed a mix of relaxed and intensified selection among plastome genes, but most genes under selection pressure were not associated with transferred sequences. Notably, conserved synteny between transferred genes and plastome-derived tRNAs suggests that tRNA-mediated recombination may have facilitated these integrations prior to severe plastome degradation. CONCLUSION: It is revealed that plastome-derived gene integration into the mitogenome in C. shikokiana does not coincide with accelerated evolutionary rates or altered selection pressure. This suggests that intracellular gene transfer (IGT) may occur independently of functional constraint or adaptive significance. Despite extensive plastome degradation, the conserved mitogenome gene content in C. shikokiana underscores the evolutionary resilience of mitochondrial genomes. This study establishes a foundational reference for understanding organellar genome evolution in mycoheterotrophic orchids and highlights the need for broader mitogenomic data across Orchidaceae.