Evolutionary insights into Cordyceps militaris from mitogenome dynamics and genome-wide variation.

Cordyceps militaris is a prized entomopathogenic fungus with significant medicinal and commercial value, yet its intraspecific genetic diversity has not been thoroughly examined. Mitogenomes from 118 geographically diverse samples were analyzed to trace the evolutionary trajectory of C. militaris and elucidate the diversification of its mitochondrial genome (mitogenome). These mitogenomes are circular DNA molecules with lengths ranging from 26.5 to 40.3 kbp and GC contents ranging from 26.12% to 27.24%. Comparative mitogenomic analyses revealed conserved gene content and syntenic relationships among various samples, with intraspecific divergence primarily driven by dynamic intron turnover (including 18 identified insertion sites, with deletions outnumbering acquisitions) and high variability in intergenic regions. Evidence of mitochondrial-to-nuclear DNA transfer was also detected. Notably, the mitogenome evolved at an accelerated rate, accumulating mutations approximately 2.8-fold faster than the nuclear genome (SNP frequencies: 1.58% vs. 0.57%). Phylogenomic reconstructions based on mitochondrial and nuclear genomes yielded largely congruent topologies but with subtle discordances, reflecting the complex coevolutionary relationship between the two genomic compartments. Collectively, this study provides a comprehensive view of mitogenome architecture and evolutionary dynamics in C. militaris, reveals substantial organellar genetic diversity, and underscores the critical role of mitogenomes in understanding organelle-nuclear coevolution.