Comparative analysis of mitochondrial genome between two flower color of Chrysanthemum indicum

Chrysanthemum indicum is a perennial herb that is valued for its multifaceted medicinal and ornamental properties. Intraspecific variation in floral traits, most notably flower color, is common in wild and cultivated populations. To reveal the complex evolutionary characteristics and processes of Chrysanthemum mitogenomes, study the intraspecific variation, we assembled complete mitochondrial genome of two diploid C. indicum exhibiting white and yellow corollas and compared them with the previously published organellar genomes between diploid and tetraploid Chrysanthemum indicum . A hybrid assembly approach that integrated Illumina short reads with PacBio HiFi long reads produced two mitogenomes of 208,791 bp and 208,787 bp (GC content 45.50%). Each genome contained 32 protein-coding genes, 17 tRNAs and three rRNAs, together with 149 pairs of repetitive sequences ≥ 30 bp. Whole-genome alignment and gene-order comparison detected no structural rearrangements or consistent single-nucleotide differences between the color variants, indicating exceptional mitochondrial sequence conservation at the intraspecific level. Phylogenetic reconstruction based on 26 core mitochondrial protein-coding genes placed both morphs within a well-supported Chrysanthemum clade that was congruent with current angiosperm classification systems. These high-quality, annotated mitogenomes expand the genomic resource base for Chrysanthemum and provide a robust reference for future investigations into the molecular evolution, cytoplasmic inheritance, germplasm authentication, and breeding of this economically important species.