Mitochondrial genomes of four <i>Dendrobium</i> species (Orchidaceae): a comprehensive analysis of structural diversity, synteny, and plastid-derived sequences

Mitochondrial genomes (mitogenomes) in plants exhibit substantial structural diversity, offering insights into evolutionary processes such as intracellular gene transfer (IGT), gene loss and genomic rearrangements. In this study, we present a detailed comparative analysis of the mitogenomes of four <italic>Dendrobium</italic> species (<italic>D. lasianthera</italic>, <italic>D. tangerinum</italic>, <italic>D. huoshanense</italic> and <italic>D. chrysotoxum</italic>), which are from the highly diverse Orchidaceae family. Using high-quality read data, including Illumina, PacBio and HiFi reads, we assembled and annotated their complete mitogenomes. Our findings reveal notable variability in mitogenome size (ranging from 485,249 to 773,276 bp), gene content (including differences in the number of protein-coding genes and tRNAs) and structural organization (such as conserved syntenic blocks and rearranged regions), reflecting the dynamic evolution of mitogenomes among these <italic>Dendrobium</italic> species. Notably, we observed high levels of simple sequence repeats (SSRs), with variations in repeat content across species, reflecting the dynamic nature of these genomes. Synteny analysis revealed extensive conserved genomic regions between the mitogenomes of <italic>D. lasianthera</italic> and <italic>D. tangerinum</italic>, indicating strong structural similarity. In contrast, other species pairs such as <italic>D. lasianthera</italic> and <italic>D. huoshanense</italic>, or <italic>D. tangerinum</italic> and <italic>D. chrysotoxum</italic>, exhibited weaker syntenic relationships, reflecting a greater degree of structural variation in their mitogenomes. Furthermore, our analysis identified IGT between mitogenome and plastome, providing clear evidence that IGT has contributed to the mitogenome evolution of these species. Phylogenetic analysis based on mitogenome coding sequences (CDSs) revealed a well-supported topology within <italic>Dendrobium</italic>, identifying <italic>D. lasianthera</italic> and <italic>D. tangerinum</italic> as closely related sister species. Although our sampling is limited to four <italic>Dendrobium</italic> species, the mitogenome CDS data still provide informative phylogenetic signals and offer complementary insights when interpreted alongside plastid-based phylogenies. This study provides new insights into the structural and genomic diversity of mitogenomes in <italic>Dendrobium</italic> and contributes to the broader understanding of mitogenome evolution in plants.