The complexity of the mitochondrial genome of Atractylodes macrocephala: Nanopore sequencing reveals DNA recombination and dynamic evolution

Background: The mitochondrial genome of plants is known for its complex structure and dynamic evolution. However, there is still a lack of research on the mitochondrial genome of the medicinal plant Atractylodes macrocephala. This study is the first to complete the complete analysis of the mitochondrial genome of the important medicinal herb Atractylodes macrocephala, filling the knowledge gap in this field. Methods: By integrating Oxford Nanopore long-read sequencing data and Illumina short-read sequencing data, a high-quality genome was obtained through the Flye-Unicycler mixed assembly strategy. Functional elements were annotated using tools such as PMGA and tRNAscan-SE, and RNA editing sites were predicted using Deepred-mt. The evolutionary dynamics were revealed through repeat sequence analysis, phylogenetic reconstruction, and co-linearity comparison. Results: A 420,733 bp multi-branch non-circular structure (GC content 44.22%) was assembled, containing 6 contigs. 32 unique protein-coding genes (including 24 core genes), 21 tRNAs, and 3 rRNAs were annotated. The ccmB gene was detected to have the most RNA editing sites (37). 146 SSRs, 60 tandem repeats, and 179 scattered repeats (the longest being 2,457 bp) were detected. 10.53% of the sequence (44.3 kb) was a chloroplast transfer segment (MTPTs), and 520 C-to-U type RNA editing sites were significantly enriched in the ccmB and mttB genes. The phylogenetic tree supported that Atractylodes macrocephala belongs to the Asteraceae family and the topology was consistent with the APG classification. The co-linearity analysis revealed that there were a large number of genomic rearrangements (inverted regions accounting for 25-66%) between Atractylodes macrocephala and its related species (such as Arctium tomentosum, Ainsliaea angustata). Conclusion: This study first revealed the complex structure of the mitochondrial genome of Atractylodes macrocephala and its dynamic evolution mediated by repeat sequence-mediated recombination, chloroplast DNA migration, and RNA editing. It provides new insights into the mitochondrial evolution of Asteraceae plants and lays a genetic foundation for molecular breeding and medicinal mechanism research of Atractylodes macrocephala.