Journal Article

Complete mitochondrial genome of Polygonatum cyrtonema Hua reveals variation diversity and evolutionary trends

Luo, Haoxiang, Wang, Dekai, Jia, Qiaojun, Cao, Guochao, Ren, Fengxiao

2025

Overview

Background Polygonatum cyrtonema Hua , a valuable medicinal and edible plant in China, has been increasingly cultivated to produce nutritional and health products to meet market demand. However, the absence of the mitochondrial genome hinders the research of evolutionary analysis, artificial cultivation, and medicinal resource development. This study aimed to systematically characterize the mitochondrial genome of P. cyrtonema and perform a preliminary bioinformatic analysis. Result In this study, the mitochondrial genome of P. cyrtonema was assembled and annotated by combining Illumina reads with long-read Oxford Nanopore Technologies, which formed a complex non-circular structure covering 664,991 bp in length, with 33 protein-coding genes, 20 tRNAs, and 3 rRNAs. Overall, a total of 194 simple repeats, 24 tandem repeats, and 294 dispersed repeats were identified, and 599 RNA editing sites were predicted, all of which were C-to-T types. In particular, 29 homologous fragments between the chloroplast and mitochondrial genome were detected and accounted for 2.4% of the mitochondrial genome. In addition, codon usage analysis, nucleotide diversity analysis, and Ka/Ks analysis suggested a slower rate of evolution and a relatively conserved structure of the mitochondrial genome. Phylogenetic relationships based on 33 species demonstrated that P. cyrtonema was most closely related to Polygonatum sibiricum . Conclusion Our results provide comprehensive information on the mitochondrial genome of P. cyrtonema , and demonstrate the availability of mitochondrial genome-based taxonomic classification for Polygonatum Mill.. Moreover, it offers a valuable foundation for future research in the cultivation and pharmacological development within Polygonatum species.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Agriculture / Analysis / Bats / bioinformatics / Biological evolution / Biomedical and Life Sciences / China / Chloroplasts / codon usage / Cultivation / Cytochrome / Editing / Environmental aspects / Evolution, Molecular / Evolutionary biology / food plants / Gene Expression Regulation, Plant / Genes / Genetic aspects / Genetic Variation / Genome, Mitochondrial - genetics / Genome, Plant / Genomes / Life Sciences / Medicinal plants / Medicine, Chinese Traditional / Mitochondria / Mitochondrial DNA / Mitochondrial genome / nanopores / Nucleotides / Phylogenetic evolution / Phylogenetics / Phylogeny / Plant Proteins - genetics / Plant Sciences / Plants, Edible - genetics / Plants, Medicinal - genetics / Polygonatum / Polygonatum - classification / Polygonatum - genetics / Polygonatum cyrtonema / Polygonatum cyrtonema Hua / Polygonatum sibiricum / Proteins / Repeated sequences / Resource development / resource management / RNA / RNA editing / RNA, Plant / Seeds / Software / species / supply balance / Tree Biology / Vegetables