Chloroplast genome sequencing and comparative analysis of six medicinal plants of Polygonatum
Jinchen Yao1, # | Zhaohuan Zheng1, # | Tao Xu5| Duomei Wang2 | Jingzhe Pu2 | Yazhong Zhang2*| Liangping Zha1, 3, 4*
1 College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
2 Anhui Institute for Food and Drug Control, Hefei, China
3 Institute of Conservation and Development of Traditional Chinese Medicine Resources, Anhui Academy of Chinese Medicine, Hefei, China
4 MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China
5 Biological and Pharmaceutical Engineering, West Anhui University, Luan, China
# Authors Jinchen Yao and Zhaohuan Zheng contributed equally to this work.
* Correspondence: Liangping Zha, Anhui University of Chinese Medicine, Hefei 230012, China. Email: zlp_ahtcm@126.com| Yazhong Zhang, Anhui Institute for Food and Drug Control, Hefei 230051, China. Email: 282483507@qq.com
Funding information: Excellent Young Scholars Project of Natural Science Foundation of Anhui Province in China, Grant/Award Numbers: 2208085Y30; Science Research Project at the Universities of Anhui Province for Distinguished Young Scholars, Grant/Award Numbers: 2023AH020036; the Key Project Foundation of Support Program for the Excellent Young Faculties in Universities of Anhui Province in China, Grant/Award Numbers: gxyqZD2022051; Young Elite Scientists Sponsorship Program by CACM, Grant/Award Numbers: CACM-2023-QNRC2-B23; NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Grant/Award Numbers: AHYJ-KFKY-202102; the Fund of Generic Technology Research center for Anhui Traditional Chinese Medicine Industry, Grant/Award Numbers: AHTCMGTRC-2023-06; Traditional Chinese Medicine high-level key discipline construction project of National Administration of Traditional Chinese Medicine-Science of Chinese medicinal material resources (pharmaceutical botany), Grant/Award Numbers: zyyzdxk-2023095; Scientific Research Team Program of Anhui Colleges and Universities, Grant/Award Numbers: 2022AH010036.
Abstract
The genus Polygonatum boasts abundant germplasm resources and comprises numerous species. Among these, medicinal plants of this genus, which have a long history, have garnered attention of scholars. This study sequenced and analyzed the chloroplast genomes of six species ofPolygonatum medicinal plants (P. zanlanscianense , P. kingianum , P. sibiricum , P. cyrtonema , P. filipes and P. odoratum , respectively) to explore their inter-specific relationships. The sequence length (154, 578–155, 807 bp) and genome structure were conserved among the six Polygonatum species, with a typical tetrad structure. The genomes contain 127–131 genes, containing 84–85 protein-coding genes, 37–38 transfer RNA genes, and 6–8 ribosomal RNA genes. The genomes contained 64–76 simple sequence repeats (SSRs) and 36–62 long repetitive sequences. Codon bias patterns tended to use codons ending in A/T. In thirty types of codons with RSCU > 1, 93.3% ended in A/T of the six species. Twenty-one highly variable plastid regions were identified in the chloroplast genomes of the six medicinal plants. In addition, phylogenetic analysis of these and other 53 Polygonatum chloroplast genomes showed thatP. cyrtonema , P. odoratum and P. filipes were clustered on one large clade, whereas P. kingianum and P. zanlanscianense were clustered on other clades. P. sibiricum is a monophyletic group and our tree supports the classification ofP. sibiricum as an independent clade. This study provides a novel basis for intragenus taxonomy and DNA barcoding molecular identification within the genus Polygonatum medicinal plants.
K E Y W O R D S: Polygonatum , chloroplast genome, interspecific relationships, DNA barcoding molecular identification, phylogenetic