The complete chloroplast genome of Polygonatum zanlanscianense (Pampanini, 1915) (Asparagaceae), an adulterants of Polygonati rhizoma

Abstract

Polygonatum zanlanscianense Pamp. is a plant species of the genus Polygonatum (Asparagaceae) distributed widely in China. The complete chloroplast genome of P. zanlanscianense was sequenced by Illumina sequencing technology. The plastome is 155,609 bp in length with a typical quadripartite structure, including one small single copy (SSC, 18,427 bp), one large copy (LSC, 84,438 bp), and two inverted repeat regions (IRs, 26,372 bp each). The cp genome encoded 132 genes, including 38 tRNA, 8 rRNA, and 86 protein-coding genes. The overall GC content is 37.7%. The ML phylogenetic analysis based on the cp genomes indicated that the genus Polygonatum is sister to the genus Heteropolygonatum within the tribe Polygonateae, P. zanlanscianense is sister to P. cirrhifolium within the genus Polygonatum. This study provides an important theoretical foundation for varieties identification, the phylogenetic relationship of P. zanlanscianense. Furthermore, this article takes a radical reform of Polygonati rhizoma.

Polygonati rhizoma is one of the most valuable medicinal and edible plants, which has been fully used by people since ancient times (Liu and Si 2018). Even now Polygonati rhizoma has great potential for resource development and broad market prospects for its high economic and medicinal value (Zhang et al. 2019; Liu et al. 2020). However, there are many species in the genus Polygonatum, besides it is difficult to classify and identify species (Zhao et al. 2018). In production and daily life, species of the same family are often used as the counterfeit of Polygonati rhizoma, which seriously endangers people's life and property safety. Polygonatum zanlanscianense Pamp. is one of the species in the genus Polygonatum, distributed in Gansu, Henan, Jiangsu, Hubei, Sichuan, and other provinces in China (Chen and Tamura 2000). Because of the morphology similarity between P. zanlanscianense and Polygonati rhizoma, the adulterants were mixed with P. zanlanscianense. Therefore, the study of P. zanlanscianense is conducive to the effective identification of medicinal materials and the standardization of Polygonati rhizoma market (Wang 2020).

Chloroplast is a semi-autonomous organelle responsible for photosynthesis in green plant cells (Jansen et al. 2005). It has a stable and conserved double-stranded genome, containing four parts: large single copy (LSC), small single copy (SSC), and two inverted repeats (IRs) (Wang et al. 2012). In view of the advantages of the chloroplast genome, such as easy obtainment, moderate length, monophyletic inheritance, and relatively moderate nucleic acid replacement rate, researchers have widely used it in plant phylogeny, species identification, and genetic breeding(Zhang and Li 2011; Sheng et al. 2021).

In this study, the sample was collected from Wanyuan (107°35′23″E, 31°52′46″N) at Sichuan, China. The specimen was stored in the Herbarium of Kunming Institute of Botany, Chinese Academy of Sciences (URL: http://www.kib.ac.cn/; email: jiyh@mail.kib.ac.cn, Yunheng Ji), with the voucher number JYH002. The fresh leaves of the sample were used to extract total genomic DNA using the modified CTAB method. The DNA sample was deposited in the Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences. And the sequencing library was constructed and quantified following the methods introduced by Liu et al. (2019), then sequencing was carried out using Illumina HiSeq 2500 platform. Resultant clean reads were assembled using the GetOrganelle pipeline (https://github.com/Kinggerm/GetOrganelle) with P. humile (GenBank accession no. MN218691) as the reference sequence. The assembly was edited and annotated according to the reference in Geneious V10.2. Start and stop codons and intron/exon boundaries for protein-coding genes were checked manually. The plastome sequence of P. zanlanscianense was deposited in the NCBI GenBank database (MW800891).

The P. zanlanscianense plastome presents a typical quadripartite structure consisting of one large single-copy region (LSC, 84,438 bp), one small single-copy region (SSC, 18,427 bp), and a pair of inverted repeat regions (IRs, 26,372 bp each). The overall GC content is 37.70%, and the corresponding values for LSC, SSC, and IR regions are 35.70%, 31.50%, and 42.90%, respectively. The plastome encodes 132 genes (86 protein-coding genes, 38 tRNAs, and 8 rRNAs).

We used the online software: CIPRES Gateway (http://www.phylo.org/) to construct a phylogenetic tree based on the maximum likelihood method to determine the phylogenetic position of P. zanlanscianense (Figure 1). In this study, 17 species representing eight genera were downloaded from the genebank database, Asparagus officinalis L. (NC_034777) was taken as an outgroup. The results showed that the genus Polygonatum was closely related to Heteropolygonatum within the Tribe Polygonateae; P. zanlanscianense was sister to P. cirrhifolium, which may be related to their transitional morphology and overlapping geographical distribution.

Figure 1.

Phylogenetic relationships of P. zanlanscianense with other Polygonatum species. 

Funding Statement

This study was financially supported by National Natural Science Foundation of China [81360611].

Disclosure statement

The authors declare no potential conflict of interests.

Data availability statement

The data that support the findings of this study are openly available in GenBank at https://www.ncbi.nlm.nih.gov, reference number [MW800891]. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA722812 SRR14270298 and SAMN18793888, respectively.