The Structure, Evolution, and Comparative Genomics of the Dendrobium officinale Mitochondrial Genome

Abstract

Dendrobium officinale is an important medicinal Orchidaceae species with considerable ecological and economic value. While its chloroplast genome has been well characterized, the structure features of its mitochondrial genome remain largely unexplored, which further hinders our understanding of its evolutionary dynamics and adaptive mechanisms. This study presents a comprehensive characterization of the mitochondrial genome of D. officinale, revealing a complex multibranched structure of 22 chromosomes totaling 639,931 bp, encoding 35 PCGs, 3 rRNA genes, and 24 tRNA genes. Codon usage analysis revealed a distinct codon bias, while the genome harbors abundant repetitive elements and 522 RNA editing sites. Comparative genomic analysis identified 125 MTPT fragments totaling 108,012 bp (16.88% of the mitogenome), indicating frequent inter-organellar DNA transfer. Dendrobium nobile exhibited the highest genomic homology with D. officinale. Ka/Ks analysis indicated that most mitochondrial genes are under strong purifying selection. In addition, we conducted a comparative analysis between the newly assembled mitochondrial genome of D. officinale and seven Orchidaceae species. Phylogenetic analysis based on the maximum likelihood, maximum parsimony and bayesian inference approaches resolved the phylogenetic position of D. officinale within Orchidaceae. Collectively, these findings provide a valuable reference for future studies on Orchidaceae phylogenomics and mitochondrial evolution.