Unveiling the complete organelle genomes of Gypsophila vaccaria: de novo assembly and evolutionary insights into a medicinally important species

TL;DR

This paper presents the first complete mitochondrial and chloroplast genomes of Gypsophila vaccaria, a medicinal plant, revealing evolutionary insights and molecular markers.

Contribution

The study provides the first organellar genomes for Gypsophila, uncovering novel mitochondrial DNA transfers and adaptive gene selection.

Findings

The mitochondrial genome contains 56.7 Kb of chloroplast DNA transfers, the highest in Caryophyllaceae.

Positive selection was detected in cytochrome c maturation genes, contrasting with overall purifying selection.

81 species-specific SSR markers were identified for molecular breeding in Caryophyllaceae.

Abstract

Gypsophila vaccaria (Caryophyllaceae) is a medicinal plant with over 2,000 years of documented use in China. Despite its known pharmacological properties and phytochemical profile, no organellar genomic resources are currently available, limiting evolutionary studies and molecular breeding efforts.

We assembled the complete mitochondrial (361,814 bp) and quadripartite chloroplast (150,050 bp) genomes of G. vaccaria using HiFi sequencing. Codon usage, RNA editing, and selection pressure were analyzed, and phylogenomic relationships were inferred. Species-specific SSR markers were identified for potential molecular applications.

HiFi-based assembly revealed exceptional mitochondrial genome plasticity, with 15.6% (56.7 Kb) derived from chloroplast DNA transfers—the highest reported in Caryophyllaceae—including 12 functional genes (e.g., rps7, ndhB, rrn16S). Both organellar genomes show A/U-biased codon usage (mitochondrial RSCU: 29/44 codons) and divergent RNA editing (257 mitochondrial vs. 105 chloroplast C-to-U sites). Positive selection (Ka/Ks > 1) was detected in cytochrome c maturation genes (ccmFN, ccmB, ccmFC), contrasting with overall purifying selection (median ω = 0.32). Phylogenomic analyses robustly resolved Caryophyllaceae–Amaranthaceae sisterhood (BS = 100%).

As the first organellar genomes from Gypsophila, this study provides insights into lineage-specific adaptations through chloroplast-mitochondrial co-evolution. The 56.7 Kb MTPTs and positively selected cytochrome c genes serve as targets for adaptive evolution research, while 81 species-specific SSRs facilitate molecular marker development in Caryophyllaceae.

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