Unraveling the mitochondrial genome of the medicinal Chinese motherwort (Leonurus japonicus, Lamiaceae): structural dynamics, organelle-to-nuclear gene transfer, and evolutionary implications

Abstract

Introduction: Leonurus japonicus (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.

Methods: We assembled the complete mitochondrial genome of L. japonicus using a combination of Oxford Nanopore long reads and Illumina short reads. Three assembly strategies-de novo assembly with PMAT and Flye, and hybrid assembly with Unicycler-were integrated and validated via read mapping and comparison to reference mitogenomes (Salvia miltiorrhiza, Arabidopsis thaliana, Liriodendron tulipifera). 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.

Results: 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 L. japonicus among Lamiales, closely allied to Scutellaria tsinyunensis and Rotheca serrata. Synteny maps demonstrated frequent genome rearrangements. Deepred-mt predicted 408 C-to-U RNA editing sites, notably in nad4 and ccmB, including novel start and stop codons.

Discussion: The L. japonicus 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 Leonurus, support phylogenetic and evolutionary studies in Lamiaceae, and lay groundwork for molecular breeding and conservation strategies targeting mitochondrial traits.

Keywords: Leonurus japonicus; RNA editing; long-read sequencing; mitochondrial genome; phylogenetic relationships; plastid-derived DNA; repeat sequence; synteny analysis.

Figure 1

The putative circular mitogenome maps of L. japonicus. Different color blocks represent various functional gene groups.

Figure 2

The simple sequence repeats (SSRs) and dispersed repeats identified in the mitogenome of L. japonicus. (A) The SSRs identified in the L. japonicus mitogenome, with each column representing different nucleotide repeat units displayed in various colors. (B) Dispersed repeats (≥ 30 bp) identified in the L. japonicus mitogenome.

Figure 3

Relative synonymous codon usage (RSCU) analysis of mitochondrial and plastid protein-coding genes in L. japonicus. Left: mitochondrial; Right: plastid.

Figure 4

Phylogenetic analyses of L. japonicus based on mitogenome. The plants in the diagram belong to the order Lamiales. Different orders are represented by different colors, with L. japonicus represented in red.

Figure 5

The collinear blocks among mitogenomes. Bars indicated the mitogenomes, and the ribbons showed the homologous sequences (> 500 bp) between the adjacent species. The red areas and gray areas indicate collinear blocks with inconsistent and consistent arrangement orders, respectively.

Figure 6

Schematic representation of homologous sequences between the plastome and mitogenome in L. japonicus. Blue arcs represent mitogenome, green arcs represent the plastome, and the lines between arcs correspond to homologous genome segments.

Figure 7

Homologous genes from L. japonicus organelle genomes on nuclear chromosomes are labeled. Icons near the chromosomes indicate the positions of genes from organelles (plastids and mitochondria, distinguished by purple and blue colors) on chromosomes. Genes are divided into CDS, rRNA, and tRNA types and are distinguished by three shapes (circle, square, and triangle). Complete and partial genes were indicated with dark and light colors, respectively. The percentage numbers below the chromosomes represent the percentage of the length of the homologous segment on that chromosome, with blue numbers representing the plastid homologous segment and pink numbers representing the mitochondrial homologous segment.

Figure 8

Characteristics of the RNA editing sites identified in protein-coding genes (PCGs) of L. japonicus mitogenome. Number of RNA editing sites predicted by individual PCGs using Deepred-mt. The x-axis shows the gene names, and the y-axis shows the number of edited sites.