Abstract
Claviceps purpurea 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 C. purpurea strains isolated from different host plants, including seven newly sequenced isolates from China. Analysis of the C. purpurea 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 atp9 gene was absent in all strains, suggesting a potential adaptive gene loss. Structural variations were predominantly located in the intergenic region between rns and rnl. Phylogenetic analysis based on concatenated mitochondrial genes placed Claviceps as most closely related to the genus Epichloë. The 15 C. purpurea 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 C. purpurea and highlights the value of mitogenome in resolving phylogenetic relationships.