Pan-Mitogenome Construction, Intraspecific Variation, and Adaptive Evolution of the Plant Pathogenic Fungus Claviceps purpurea

<i>Claviceps purpurea</i> is a specialized phytopathogenic fungus that infects grasses and produces pharmacologically active compounds, attracting considerable interest in genomic research. In this study, we assembled and annotated the complete mitogenomes of 15 <i>C. purpurea</i> strains isolated from different host plants, including seven newly sequenced isolates from China. Analysis of the <i>C. purpurea</i> pan-mitogenome demonstrated that the accessory regions, with an average proportion of 48.23%, are the main contributor to mitogenome variation. Analysis of the 14 protein-coding genes revealed Ka/Ks ratios below 1, indicating strong purifying selection. Notably, the <i>atp9</i> gene was absent in all strains, suggesting a potential adaptive gene loss. Structural variations were predominantly located in the intergenic region between <i>rns</i> and <i>rnl</i>. Phylogenetic analysis based on concatenated mitochondrial genes placed <i>Claviceps</i> as most closely related to the genus <i>Epichloë</i>. The 15 <i>C. purpurea</i> strains grouped into five well-supported subclades, with Chinese and non-Chinese isolates forming distinct lineages. Among these, the Chinese strains ACCC 37001 and KUNCC 11030 represented the earliest diverging lineages. This study elucidates the intraspecific variation and evolutionary patterns of the mitogenome in <i>C. purpurea</i> and highlights the value of mitogenome in resolving phylogenetic relationships.