Background: Centella asiatica, a medicinally important species that is rich in bioactive compounds, lacks a characterized mitochondrial genome, despite nuclear and chloroplast assemblies. We sequenced and annotated its mitochondrial genome to elucidate its genetic foundations and evolutionary mechanisms. Methods: Assembly using Illumina short-reads and Nanopore long-reads was used to characterize the mitochondrial genome. Analyses included structural characterization, codon usage bias, repetitive sequences, horizontal gene transfer (HGT), collinearity, and phylogeny. The resulting tissue-specific (root, stem, and leaf) long non-coding RNA (lncRNA) profiles identified RNA editing sites. Results: The complete mitochondrial genome (249,777 bp, 45.5% GC) comprises three circular contigs encoding 51 genes (33 protein-coding, 15 tRNA, and 3 rRNA). Comparative genomics revealed synteny with the Apiaceae family of plants and evidence of HGT. Phylogenetic analysis resolved taxonomic relationships within Apiales. We predicted that 547 RNA editing sites would be identified in its protein-coding genes. Tissue profiling identified 725 (root), 711 (stem), and 668 (leaf) editing sites, with >71% concordance to predictions. RNA editing-generated cryptic promoters/terminators occur in mitochondrial core function genes (e.g., ATP synthase, cytochrome c reductase/oxidase, ribosome large subunit, and cytochrome c biogenesis), exhibiting a lower frequency in the leaves compared to the roots and stems. Conclusions: We provide the first complete mitochondrial genome assembly for C. asiatica, delineating its complex structure, tissue-modulated RNA editing, and evolutionary trajectory. This high-quality genomic resource establishes a foundation for molecular evolutionary studies and enhances the genomic toolkit for this pharmacologically significant species.

The size of the mitogenome varies greatly in angiosperms from different species, but the causes of expansion remain unclear. Species from the Zingiberaceae family often carry exceptionally large mitogenomes, where this phenomenon can be readily studied. C. kwangsiensis is a medicinal plant that is native to Guangxi, China, and it is traditionally used to treat blood stasis and gynecological conditions. We assembled its complete mitogenome by using the Illumina and Nanopore reads obtained from its analysis. The genome comprises 12 circular contigs with a multi-branched structure, totaling 7.76 Mb. It contains 39 protein-coding genes, 30 tRNAs (transfer RNAs), three rRNAs (ribosomal RNAs), and 652 C-to-U RNA edited sites. Repeated analysis revealed that the dispersed repeats are the major contributors to genome expansion. Comparisons with two other Zingiberaceae mitogenomes suggested that the large genome arose in a common ancestor rather than from a whole-genome duplication, with little contribution from DNA transfers from the chloroplasts and nuclei. Thus, the exceptionally large mitogenome of Curcuma appears to result largely from repeated accumulation in the non-coding regions, such as nuclear genome expansion in angiosperms. This finding also highlights the conservation of core mitochondrial genes. Our work provides new insights into mitogenomic size variations and gene conservation in plant species, including Zingiberaceae.

As an early-diverging angiosperm lineage, Chloranthaceae produces specialized coumarins with documented antimicrobial and anti-inflammatory activities, which contribute to its ecological success. Isofraxidin, the most representative dihydroxycoumarin in this clade, exhibits significant pharmaceutical potential. However, its biosynthetic basis remains uncharacterized. Here, we assembled a high-quality triploid genome of Chloranthus erectus (8.57 Gb, contig N50=8.76 Mb) to explore the evolution of defensive metabolism. Genomic analysis revealed an ancient WGD event and expanded gene families associated with pathogen resistance. Metabolomic analysis identified at least 49 coumarin compounds in Chloranthus plants, significantly exceeding previous records. Integrated omics revealed 267 candidate biosynthetic genes across 9 enzyme families governing isofraxidin biosynthesis. PAL-4CL established the phenylpropanoid backbone, amplified COSY genes correlated with umbelliferone accumulation, and CYP71/OMT catalyzed terminal modifications. This study deciphers the chemical defense evolution in early angiosperms and enables engineering of plant-derived antimicrobials.