Bai Xinyu, Zhu Tingting, Chen Huiru, Wang Xiaoqun, Liu Jing, Feng Yuqing, Huang Yanbo, Lee Joongku, Kokubugata Goro, Qi Zhechen, Yan Xiaoling
Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China.
Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.
Front Plant Sci. 2025 Jun 3;16:1546449. doi: 10.3389/fpls.2025.1546449. eCollection 2025.
(Chinese motherwort) is a medicinal Lamiaceae species renowned for its pharmacological compounds, yet its mitochondrial genome remains unexplored. Elucidating mitogenomic structure and evolution can inform plant genetics, phylogenetics, and molecular breeding.
We assembled the complete mitochondrial genome of using a combination of Oxford Nanopore long reads and Illumina short reads. Three assembly strategies- assembly with PMAT and Flye, and hybrid assembly with Unicycler-were integrated and validated via read mapping and comparison to reference mitogenomes (). Annotation employed GeSeq, tRNAscan-SE, and manual curation. Repeat elements (SSR, tandem, dispersed) were identified with MISA, TRF, and REPuter; plastid-to-mitochondrion transfers (MTPTs) were detected by BLASTN against the assembled plastome; and RNA editing sites were predicted using Deepred-mt. Phylogenetic and synteny analyses were conducted with IQ-TREE, MAFFT alignments of 24 conserved PCGs, and NGenomeSyn visualization.
The circular mitogenome spanned 384,199 bp (45.1% GC) and encoded 35 protein-coding genes, 11 tRNAs, and 3 rRNAs. We detected 241 SSRs, 13 tandem repeats, and 90 dispersed repeats, indicating extensive recombination potential. Thirty-one MTPTs totaling 24,818 bp (6.46% of the mitogenome) were identified. Comparative analyses revealed strong purifying selection (Ka/Ks < 1) across most PCGs, with selective signatures in atp4 and ccmB. Phylogenetic inference placed among Lamiales, closely allied to and . Synteny maps demonstrated frequent genome rearrangements. Deepred-mt predicted 408 C-to-U RNA editing sites, notably in nad4 and , including novel start and stop codons.
The mitogenome exhibits marked structural plasticity, reflecting dynamic repeats and organelle-to-organelle DNA transfers. Extensive RNA editing underscores post-transcriptional regulation in mitochondrial function. These findings enrich genomic resources for , support phylogenetic and evolutionary studies in Lamiaceae, and lay groundwork for molecular breeding and conservation strategies targeting mitochondrial traits.
益母草是一种唇形科药用植物，以其药理成分而闻名，但其线粒体基因组仍未被探索。阐明线粒体基因组结构和进化可为植物遗传学、系统发育学和分子育种提供信息。
我们结合牛津纳米孔长读长和Illumina短读长组装了益母草的完整线粒体基因组。整合了三种组装策略——使用PMAT和Flye进行组装，以及使用Unicycler进行混合组装，并通过读段映射和与参考线粒体基因组进行比较来验证。注释采用GeSeq、tRNAscan-SE和人工校正。使用MISA、TRF和REPuter识别重复元件（简单序列重复、串联重复、分散重复）；通过针对组装的质体基因组进行BLASTN检测质体到线粒体的转移（MTPT）；并使用Deepred-mt预测RNA编辑位点。使用IQ-TREE、24个保守的蛋白质编码基因的MAFFT比对和NGenomeSyn可视化进行系统发育和共线性分析。
环状线粒体基因组跨度为384,199 bp（GC含量为45.1%），编码35个蛋白质编码基因、11个tRNA和3个rRNA。我们检测到241个简单序列重复、13个串联重复和90个分散重复，表明具有广泛的重组潜力。鉴定出31个MTPT，总计24,818 bp（占线粒体基因组的6.46%）。比较分析显示，大多数蛋白质编码基因存在强烈的纯化选择（Ka/Ks < 1），在atp4和ccmB中有选择特征。系统发育推断将益母草置于唇形目之中，与筋骨草属和龙头草属关系密切。共线性图谱显示频繁的基因组重排。Deepred-mt预测了408个C-to-U RNA编辑位点，特别是在nad4和其他基因中，包括新的起始和终止密码子。
益母草线粒体基因组表现出显著的结构可塑性，反映了动态重复和细胞器间的DNA转移。广泛的RNA编辑突出了线粒体功能中的转录后调控。这些发现丰富了益母草的基因组资源，支持唇形科的系统发育和进化研究，并为针对线粒体性状的分子育种和保护策略奠定基础。
