Mitochondrial Genome Characteristics Reveal Evolution of Danxiaorchis yangii and Phylogenetic Relationships

<i>Danxiaorchis yangii</i> is a fully mycoheterotrophic orchid that lacks both leaves and roots, belonging to the genus <i>Danxiaorchis</i> in the subtribe Calypsoinae. In this study, we assembled and annotated its mitochondrial genome (397,867 bp, GC content: 42.70%), identifying 55 genes, including 37 protein-coding genes (PCGs), 16 tRNAs, and 2 rRNAs, and conducted analyses of relative synonymous codon usage (RSCU), repeat sequences, horizontal gene transfers (HGTs), and gene selective pressure (dN/dS). Additionally, we sequenced and assembled its plastome, which has a reduced size of 110,364 bp (GC content: 36.60%), comprising 48 PCGs, 26 tRNAs, and 4 rRNAs. We identified 64 potential chloroplast DNA fragments transferred to the mitogenome. Phylogenomic analysis focusing on 33 mitogenomes, with <i>Vitis vinifera</i> as the outgroup, indicated that <i>D. yangii</i> is grouped as follows: <i>D. yangii</i> + ((<i>Dendrobium wilsonii</i> + <i>Dendrobium wilsonii henanense</i>) + <i>Phalaenopsis aphrodite</i>). Phylogenetic analysis based on 83 plastid PCGs from these species showed that <i>D. yangii</i> is grouped as follows: (<i>D. yangii</i> + <i>Pha. aphrodite</i>) + (<i>Den. wilsonii</i> + <i>Den. henanense</i>). Gene selective pressure analysis revealed that most mitochondrial and plastid genes in <i>D. yangii</i> are under purifying selection, ensuring functional stability, and certain genes may have undergone positive selection or adaptive evolution, reflecting the species' adaptation to specific ecological environments. Our study provides valuable data on the plastomes and mitogenomes of <i>D. yangii</i> and lays the groundwork for future research on genetic variation, evolutionary relationships, and the breeding of orchids.