Abstract
BACKGROUND: Vincetoxicum pycnostelma is a plant with pharmaceutical importance in traditional Chinese medicine, because its roots and rhizomes contain abundant anti-tumor and anti-inflammatory active compounds. Although sequencing its organelle genomes is critical to understand the genetic basis of these medicinal traits and advance molecular breeding programs, the mitochondrial genome (mtDNA) of V. pycnostelma has not yet been reported. RESULTS: Here, we sequenced and assembled the organelle genomes of V. pycnostelma with PacBio and BGI sequencing technologies, and conducted a comprehensive comparative genomic analysis. The complete mtDNA (703,719 bp, GC content 43.98%) encoded 38 protein-coding genes (PCGs), 18 tRNAs, and 3 rRNAs, whereas the chloroplast genome (cpDNA; 159,426 bp, GC content 37.85%) contained 79 PCGs, 29 tRNAs, and 4 rRNAs. Codon usage analysis indicated that both the mtDNA and cpDNA exhibited conserved codon usage preferences. Additionally, both genomes contained abundant microsatellite, tandem, and dispersed repeat sequences, and cpDNA showed a more concentrated distribution of repeats. We identified 59 homologous fragments between the mtDNA and cpDNA of V. pycnostelma, including 16 complete PCGs and 5 complete tRNA genes. Phylogenetic analysis and collinearity assessments demonstrated that V. pycnostelma exhibited the closest genetic affinity to Asclepias syriaca. A comparative analysis of nucleotide diversity and boundary regions in Vincetoxicum chloroplast genomes revealed relatively conserved genomic features alongside highly variable regions. CONCLUSIONS: Our findings provide essential technical support for molecular breeding of V. pycnostelma and rapid identification of its medicinal materials, which may facilitate sustainable industrial development.