Organelle genome architecture of Salvia plebeia reveals mitochondrial recombination and evolutionary dynamics

Abstract

Introduction Salvia plebeia is a medicinal plant in Lamiaceae, but its organelle genome architecture and evolutionary dynamics remain insufficiently understood, particularly for the mitochondrial genome. Methods We assembled and analyzed the mitochondrial and chloroplast genomes of S. plebeia using PacBio HiFi long-read sequencing. Genome assembly, annotation, and correction were performed using PMAT2, Minimap2, NextPolish, and GeSeq. Repetitive elements were identified using SSR, tandem repeat, and dispersed repeat analyses. Repeat-mediated recombination was validated using long-read mapping and PCR. Comparative chloroplast genomics and phylogenetic analyses were conducted using mVISTA, MUMmer4, and IQ-TREE2. RNA-editing sites were predicted using PREPACT, and codon usage bias was analyzed using CodonW. Results The mitogenome is a 444,036 bp circular molecule encoding 58 genes, while the chloroplast genome is 151,062 bp with a typical quadripartite structure. A total of 135 SSRs, 331 dispersed repeats, and 25 mitochondrial plastid DNA transfer (MTPT) regions were identified. Six repeat pairs were experimentally supported to mediate homologous recombination, indicating alternative mitochondrial conformations. RNA-editing analysis identified 587 C-to-U sites. Phylogenetic analyses placed S. plebeia within the Salvia lineage, and plastomes showed high conservation, whereas the mitogenome exhibited extensive structural rearrangements. Discussion These findings highlight a contrast between conserved chloroplast genomes and highly dynamic mitochondrial genomes in S. plebeia, driven by repeat-mediated recombination and RNA editing, providing new insights into organelle genome evolution in Lamiaceae.