Comparative analysis of the complete multi-chromosomal mitogenome of Anoectochilus emeiensis (Orchidaceae)

Anoectochilus emeiensis K. Y. Lang, an orchid with high ornamental and medicinal value, serves as a core raw material in numerous herbal medicines owing to its pharmacological effects. In 2015, its wild populations comprised six local groups with approximately 5,000 individuals. By 2023, only two populations with fewer than 500 individuals remained, largely resulting from habitat destruction and overexploitation. Deciphering the mitochondrial genome of A . emeiensis will help elucidate the structural diversity and functional conservation of Anoectochilus mitogenomes, and offer insights into genome evolution and adaptive strategies. To date, the A . emeiensis mitogenome has not been documented. The mitogenome of A . emeiensis exhibits a multi-chromosomal structure consisting of 20 circular isoforms. Individual chromosome lengths vary from 13,437 bp to 43,704 bp, with a total length of 490,926 bp and an average GC content of 45.07%. The mitogenome harbors 29 protein-coding genes, 21 tRNA genes, and 3 rRNA genes. Codon usage analysis revealed neutral characteristics with A/U bias at the third codon position. Repetitive sequences, intracellular gene migration, genome size and structure, as well as RNA editing sites were all analyzed. These findings offer key clues for exploring the evolutionary process of multi-chromosomal mitochondria in Orchidaceae. Hybrid sequencing integrating second- and third-generation technologies enabled successful assembly of the A emeiensis mitogenome. This study deepens the understanding of multi-chromosomal mitogenomes in Orchidaceae, illuminates their evolutionary history, and provides valuable resources for germplasm conservation and breeding of this endangered herb.