Assembly of the complete mitochondrial genome of Ligusticum chuanxiong and its evolutionary implications

BACKGROUND: Plant mitochondrial genomes are structurally complex and highly variable, with frequent recombination and organelle-to-organelle DNA transfer. Ligusticum chuanxiong is an important medicinal plant, yet its mitochondrial genome remains insufficiently characterized. OBJECTIVE: To reconstruct and annotate the complete mitochondrial genome of L. chuanxiong comprehensively characterize its structure and gene content, repeat landscape, codon usage bias, RNA editing, plastid-derived DNA (MTPT), collinearity with related species, phylogenetic placement, and selection patterns. METHODS: We performed hybrid long- and short-read de novo assembly, reference-aided curation, and genome annotation (GeSeq/OGDRAW). Repeats were identified using MISA/TRF/Vmatch; codon usage bias (RSCU) was computed with CodonW; RNA editing sites were predicted with Deepred-Mt; MTPTs were detected via BLASTN and visualized by Circos; collinearity was assessed by pairwise comparisons. Phylogeny was inferred from concatenated mitochondrial core PCGs (MAFFT, IQ-TREE), and selection was evaluated with KaKs_Calculator. RESULTS: The mitogenome is a single circular molecule of 306,728 bp (GC 44.56%), containing 57 genes (33 PCGs, 2 rRNAs, 20 tRNAs). We identified 22 SSRs, 34 tandem repeats, and 2,402 pairs of dispersed repeats (> 240 kb total), indicating pronounced structural plasticity. Across 8,372 codons, codon usage shows a marked preference for A/U-ending synonymous codons (29 codons with RSCU > 1). A total of 6,738 C→U RNA editing sites were predicted, mainly at the 1st/2nd codon positions, with matR harboring the most sites (530). We detected 25 MTPTs totaling 21,375 bp (6.97% of the mitogenome). Collinearity was highest with accession PP968945.1 yet exhibited extensive block rearrangements. Phylogenetically, L. chuanxiong clusters with Saposhnikovia divaricata (low bootstrap support), and Ka/Ks profiles indicate predominant purifying selection with gene-specific variation. CONCLUSIONS: While compositionally conserved, the L. chuanxiong mitogenome is structurally dynamic due to abundant repeats and plastid-derived insertions. Extensive C→U RNA editing likely safeguards protein function. These data provide a high-quality genomic resource for Apiaceae phylogenomics and a foundation for future breeding and functional studies.