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

TL;DR

This study sequenced the complete mitochondrial genome of Gynostemma pentaphyllum, revealing its complex structure and evolutionary insights within the Cucurbitaceae family.

Contribution

The study provides the first complete mitochondrial genome of Gynostemma pentaphyllum and identifies dynamic evolutionary features and gene transfer events.

Findings

The mitogenome has a multipartite structure of six circular molecules and encodes typical mitochondrial genes.

Extensive RNA editing and chloroplast-derived gene transfer were detected, indicating active intracellular gene transfer.

Phylogenomic analysis places G. pentaphyllum closely with Thladiantha cordifolia and Momordica charantia.

Abstract

Background: Gynostemma pentaphyllum (Thunb.) Makino is an important medicinal plant within the Cucurbitaceae family. Despite its economic and pharmacological importance, genomic resources for this species remain limited. Methods: We sequenced and assembled the complete mitochondrial genome of G. pentaphyllum. 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. Results: 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 G. pentaphyllum firmly within Cucurbitaceae, clustering it with Thladiantha cordifolia and Momordica charantia, whereas synteny comparisons reveal pronounced structural rearrangements with respect to these close relatives. While most genes evolve under strong purifying selection, rps1, sdh3, and sdh4 show signatures of accelerated evolution; furthermore, haplotype networks based on conserved loci further corroborate the close affinity with T. cordifolia. Conclusions: This study provides the first high-resolution mitogenome resource for G. pentaphyllum and candidate mitochondrial markers for species authentication, evolutionary studies, and breeding in Gynostemma and related cucurbits.

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