Assembly and comparative analysis of the multipartite mitochondrial genome of Curcuma wenyujin reveals sequence divergence, structural variation, and phylogenetic placement within Commelinales
Curcuma wenyujin, a perennial herb known for its ornamental and medicinal properties, is a traditional Chinese medicine used for treating rheumatic immune diseases, yet its mitochondrial genome has yet to be studied. This research gap substantially restricts the comprehensive exploration of its genomic resources and phylogenetic relationships. To fill this gap, we assembled and annotated the mitochondrial genome of C. wenyujin using a combination of second- and third-generation sequencing technologies. Our results show that the mitochondrial genome is predominantly composed of 26 linear DNA molecules and one circular DNA molecule, with a total length of 7,856,194 bp and a GC content of 43.91%. We identified 125 genes, 90,107 simple repeats, 6,629 tandem repeats, 81,307 dispersed repeats, 2,171 SSRs, and 506 RNA editing sites in the genome. Most protein-coding genes initiate with the canonical ATG start codon, and a strong preference for A or T (U) at the third codon position was observed. The codons UUU, AUU, and UUC are the most frequently used in the mitochondria of C. wenyujin. Codon usage bias analysis revealed a strong preference for A/T-ending codons (87.1% of preferred codons), consistent with the conserved pattern observed in angiosperm mitochondrial genomes. Furthermore, phylogenetic analysis was performed based on 24 representative plant species, revealing a close genetic relationship between C. wenyujin and Pontederia crassipes within the order Commelinales. Comparative analyses with the congener Curcuma amarissima (Zingiberaceae) further supported high evolutionary conservation of mitochondrial genomes in the ginger family. This study represents the first comprehensive report on the mitochondrial genome of C. wenyujin, laying a solid foundation for future studies on its crop genetics and molecular breeding.