Comparative analysis of complete mitochondrial genomes from Curcuma longa and Curcuma kwangsiensis reveals structural plasticity, conserved core genes, and species-specific evolutionary dynamics.

The Zingiberaceae (ginger family) comprises economically and medicinally important plants, yet mitochondrial genome evolution within this family remains poorly understood. Curcuma longa and Curcuma kwangsiensis are widely used medicinal species whose mitogenomic architectures, gene content, and evolutionary trajectories have not been fully characterized. Understanding these features is essential to resolve phylogenetic relationships and elucidate mechanisms of mitochondrial genome plasticity. We sequenced and assembled the complete mitochondrial genomes of C. longa and C. kwangsiensis, revealing highly expanded and fragmented architectures of 7.66 Mb and 7.96 Mb, respectively. Both genomes exhibited conserved GC content (43.7-43.9%) and retained 39 core protein-coding genes, while showing species-specific variation in gene duplication, rRNA/tRNA copy numbers, and the pseudogenization of sdh3 and rpl10. Codon usage analysis indicated a strong A/U bias in synonymous positions, reflecting translational optimization. Extensive RNA editing, predominantly C-to-U conversions, increased hydrophobic residues in membrane-associated proteins, likely enhancing respiratory efficiency. Repeat analysis identified a significantly more robust repeat landscape in C. kwangsiensis, which featured 3,059 dispersed repeats in the 300 to 349 bp range and large repeats exceeding 700 bp, whereas repetitive elements in C. longa were fewer and predominantly restricted to the first molecule. Sequence divergence analysis revealed that most genes are under strong purifying selection, whereas a limited subset including atp8, ccmFn, cox2, matR, nad4, nad7, and rpl5 showed episodic positive selection. Whole-genome synteny comparisons indicated profound structural rearrangements and low collinearity, despite high sequence identity within conserved blocks (97.7%). Moreover, both species incorporated 25 plastid-derived fragments, with differences in gene completeness, highlighting ongoing cross-organelle gene transfer. Phylogenetic reconstruction placed both species within a well-supported monophyletic clade with maximum bootstrap support of 100, revealing a sister-taxa relationship between C. longa and C. amarissima while exhibiting a low substitution rate of 0.004 per site. Our study demonstrated that Curcuma mitogenomes combine remarkable structural plasticity with functional conservation. Conserved core genes, codon usage bias, and extensive RNA editing maintained mitochondrial function, while repetitive sequence proliferation, repeat-mediated recombination, and plastid-derived sequences facilitated lineage-specific diversification despite stable phylogenetic relationships. These findings provide essential genomic resources for the genus Curcuma and offer insights into mitochondrial genome evolution and species-specific diversification in Zingiberaceae.