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<InlineEquation ID="IEq1"><EquationSource Format="TEX">\(\rightarrow\)</EquationSource></InlineEquation>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<InlineEquation ID="IEq2"><EquationSource Format="TEX">\(\rightarrow\)</EquationSource></InlineEquation>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.

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

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2026年7月14日

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Zhengkun Gan,
Yanghuan Xing,
Yun Zhen,
Aien Tao,
Guihua Jiang

摘要

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\(\rightarrow\)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\(\rightarrow\)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.