Comparative analysis of the medicinal plant Polygonatum kingianum (Asparagaceae) with related verticillate leaf types of the Polygonatum species based on chloroplast genomes

Naixing Shi; Zefen Yang; Ke Miao; Lilei Tang; Nian Zhou; Pingxuan Xie; Guosong Wen

doi:10.3389/fpls.2023.1202634

Comparative analysis of the medicinal plant Polygonatum kingianum (Asparagaceae) with related verticillate leaf types of the Polygonatum species based on chloroplast genomes

Front Plant Sci. 2023 Aug 23:14:1202634. doi: 10.3389/fpls.2023.1202634. eCollection 2023.

Authors

Naixing Shi¹, Zefen Yang¹, Ke Miao², Lilei Tang³, Nian Zhou², Pingxuan Xie³, Guosong Wen¹

Affiliations

¹ College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China.
² Chinese Academy of Sciences (CAS) Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
³ College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China.

Abstract

Background: Polygonatum kingianum has been widely used as a traditional Chinese medicine as well as a healthy food. Because of its highly variable morphology, this medicinal plant is often difficult to distinguish from other related verticillate leaf types of the Polygonatum species. The contaminants in P. kingianum products not only decrease the products' quality but also threaten consumer safety, seriously inhibiting the industrial application of P. kingianum.

Methods: Nine complete chloroplast (cp) genomes of six verticillate leaf types of the Polygonatum species were de novo assembled and systematically analyzed.

Results: The total lengths of newly sequenced cp genomes ranged from 155,437 to 155,977 bp, including 86/87 protein-coding, 38 tRNA, and 8 rRNA genes, which all exhibited well-conserved genomic structures and gene orders. The differences in the IR/SC (inverted repeats/single-copy) boundary regions and simple sequence repeats were detected among the verticillate leaf types of the Polygonatum cp genomes. Comparative cp genomes analyses revealed that a higher similarity was conserved in the IR regions than in the SC regions. In addition, 11 divergent hotspot regions were selected, providing potential molecular markers for the identification of the Polygonatum species with verticillate leaf types. Phylogenetic analysis indicated that, as a super barcode, plastids realized a fast and efficient identification that clearly characterized the relationships within the verticillate leaf types of the Polygonatum species. In brief, our results not only enrich the data on the cp genomes of the genus Polygonatum but also provide references for the P. kingianum germplasm resource protection, herbal cultivation, and drug production.

Conclusion: This study not only accurately identifies P. kingianum species, but also provides valuable information for the development of molecular markers and phylogenetic analyses of the Polygonatum species with verticillate leaf types.

Keywords: Polygonatum; Polygonatum kingianum; chloroplast genome; comparative analysis; phylogenetic analysis; verticillate leaf.