The polycyclic mitochondrial genome of Angraecum sesquipedale mediated by intricate repetitive and diverse sequence compositions

BACKGROUND: Angraecum sesquipedale (DC.) Danser (commonly called Darwin's orchid) is an ornamental horticultural wild plant with ecological, economic, and evolutionary research value. While its chloroplast and nuclear genome sequence have been reported, the mitochondrial genome research remains absent. To analyze the genetic variation foundation of Darwin's orchid at the genomic level, this study utilizes genomic data of 45.38 Gigabase Illumina and 36.79 Gigabase PacBio HiFi sequencing in CNCB (PRJCA030186), to decipher the mitochondrial genome structure, composition, and sequence variation patterns of this plant. RESULTS: Herein, the A. sesquipedale mitochondrial genome length was 711,372 bp, composing of 14 circular DNAs and including 38 protein-coding, 30 tRNA, three ribosomal RNA genes, and two pseudo-genes. Its sub-mitochondrial genome length ranges among Circle 1 and Circle 14 were from 23,873 bp to 105,231 bp, and the GC content ranges from 39.22% to 44.41%, respectively. In total, 216 SSR, 103 tandem, and 1019 dispersed repeats are discriminated. RNA editing site prediction revealed 709 RNA editing events. Codon usage analysis indicated a preference for A/T (U) codon ending. Intergenomic DNA transfer was identified in all of the 14 chromosomes, with chloroplast DNA transfer fragments accounting for 11.03% of the mitochondrial genome. Comparative analysis showed that GC content is conserved, but their structure, size, and gene content of mitochondrial genome chromosomes vary significantly. Phylogenetic analysis showed that Hygrochilus parishii clustered with A. sesquipedale, indicating that the two were closely related. The relationship is agreement with the evolutionary history and taxonomic status of Darwin's Orchid. Compared to the A. sesquipedale mitochondrial genomes and other reported Orchidaceae plants, the mitochondrial genome of Darwin's Orchid has lost three ribosomal protein-coding genes and sdh3. CONCLUSION: The mitochondrial genome characteristics and phylogenetic evolution relationship of Darwin's orchid were analyzed, providing a reference basis for enhancing germplasm identification, resource diversity development, utilization, and new variety breeding research.