A comprehensive analysis of the complete Dendrobium chrysotoxum mitogenome reveals a multiple-circular structure and horizontal gene transfer from fungi

Dendrobium chrysotoxum, a perennial medicinal and horticulture plant in the genus Dendrobium within the orchid family (Orchidaceae), holds significant medicinal, ornamental, and scientific value, and thus it is recognized as an innovative horticultural crop. Despite its importance, the mitochondrial genome (mitogenome) of D. chrysotoxum, remains unexamined in the current scientific literature. In this study, we assembled an annotation of the complete mitogenome of D. chrysotoxum, which comprises 18 circular chromosomes with a total length of 582,418 bp. The mitogenome encodes a total of 63 genes including 37 protein-coding genes (PCGs), three rRNA genes, and 18 tRNA genes. Comparative analyses with other angiosperms revealed variations in gene content. Notably, our analysis revealed the retention of sdh4 in the D. chrysotoxum mitogenome, and it has contracted to 153 bp. Using RNA editing sites, we predicted a total of 605 editing sites across all PCGs, with the nad4 gene exhibiting the highest number of sites at 57. Our research further identified the extensive presence of mitochondrial plastid DNA sequences, with 87 fragments accounting for 12.75% of the mitogenome. Phylogenetic and synteny analyses further elucidated the evolutionary dynamics and rearrangement events in D. chrysotoxum as compared to other Dendrobium species. Additionally, we identified a 5,601 bp secondary horizontal gene transfer event involving fungal genes and tRNA genes. Our results provide valuable insights into the symbiotic relationships between orchids and fungi and aids in further research on its potential applications as a medicinal herb with ornamental value.