Assembly and comparative analysis of the complete mitochondrial genome of a orchid cultivar ‘Jingzi’ reveals multichromosomal architecture and plastid-derived DNA transfers

Orchidaceae is one of the most diverse flowering plant families in angiosperms and holds significant cultural, economic, and ecological value in China. Despite economic and horticultural significance, the mitochondrial genomes of Cymbidium kanran remain poorly characterized. We assembled and annotated the complete mitochondrial genome of a new orchid variety, ‘Jingzi’, using PacBio HiFi sequencing technology. The mitochondrial genome is 704, 624 bp in length with a GC content of 43.91%, comprising 24 circular contigs. It contains 38 protein-coding genes (PCGs), including 24 unique core mitochondrial genes, 27 tRNA genes, and 3 rRNA genes. Notably, atp6 exhibits an unprecedented duplication event. Intracellular gene transfer analysis revealed 91 fragments homologous between mitochondria and chloroplasts, totaling 92, 762 bp (13.16% of the mitochondrial genome). Based on 24 conserved PCGs from 20 angiosperm species, our phylogenetic analysis indicated a potential affinity between ‘Jingzi’ and Paphiopedilum from Shenzhen. Given the poor sampling of closely related genera within Cymbidium, this observation is preliminary and awaits validation from future studies with expanded taxon coverage. This study elucidates the main features of the ‘Jingzi’ mitochondrial genome, highlights extensive mitochondrial-chloroplast homology, and reports the presence of two copies of atp6 in the mitochondrial genome. These findings provide valuable insights for genetic and evolutionary studies of orchids.