The Complete Mitochondrial Genome of <i>Gynostemma pentaphyllum</i> Reveals a Multipartite Structure and Dynamic Evolution in Cucurbitaceae

<h4>Background</h4><i>Gynostemma pentaphyllum</i> (Thunb.) Makino is an important medicinal plant within the Cucurbitaceae family. Despite its economic and pharmacological importance, genomic resources for this species remain limited.<h4>Methods</h4>We sequenced and assembled the complete mitochondrial genome of <i>G. pentaphyllum</i>. Comparative analyses were conducted to investigate the genomic structure, gene content, RNA editing events, and intracellular gene transfer (IGT) from chloroplasts. Additionally, phylogenomic relationships, synteny, and the selective pressure on mitochondrial genes were evaluated against related species within Cucurbitaceae.<h4>Results</h4>The ~324 kb mitogenome has a multipartite architecture of six circular-mapping molecules. It encodes the typical complement of mitochondrial protein-coding genes, tRNAs, and rRNAs found in angiosperms. Extensive C-to-U RNA editing, including events that generate functional start and stop codons, points to substantial post-transcriptional regulation. We also detected multiple chloroplast-derived fragments, including several intact genes, indicating active intracellular gene transfer. Phylogenomic analyses of conserved mitochondrial genes place <i>G. pentaphyllum</i> firmly within Cucurbitaceae, clustering it with <i>Thladiantha cordifolia</i> and <i>Momordica charantia</i>, whereas synteny comparisons reveal pronounced structural rearrangements with respect to these close relatives. While most genes evolve under strong purifying selection, <i>rps1</i>, <i>sdh3,</i> and <i>sdh4</i> show signatures of accelerated evolution; furthermore, haplotype networks based on conserved loci further corroborate the close affinity with <i>T. cordifolia</i>.<h4>Conclusions</h4>This study provides the first high-resolution mitogenome resource for <i>G. pentaphyllum</i> and candidate mitochondrial markers for species authentication, evolutionary studies, and breeding in <i>Gynostemma</i> and related cucurbits.