| Home | E-Submission | Sitemap | Editorial Office |  
top_img
Korean J. Pl. Taxon > Volume 52(1); 2022 > Article
CHOI, YUN, and LEE: The complete chloroplast genome of Polygonatum falcatum (Asparagaceae)

Abstract

Polygonatum falcatum is a perennial herb distributed in East Asia. We determined the characteristics of the complete chloroplast genome in P. falcatum for the first time, with a de novo assembly strategy. The chloroplast genome was 154,579bp in length harboring 87 protein coding genes, 38 tRNA genes and eight rRNA genes. It exhibits typical quadripartite structure comprising a large single-copy (LSC) (83,528bp), a small single-copy (SSC) (18,457bp) and a pair of inverted repeats (IRs) (26,297bp). Phylogenetic analysis of 16 chloroplast genomes from Asparagaceae reveals that the genus Polygonatum is a monophyletic group and that P. falcatum is clustered together with the congener, P. odoratum.

INTRODUCTION

The genus Polygonatum Mill. is a diverse plant group that is particularly well appreciated in East Asia for a wide array of commercial uses, including medicinal and culinary uses (Kim et al., 2014; Floden, 2017; Zhao et al., 2017). Despite the increased recognition for its value as natural resources, knowledge on the taxonomy and phylogenetic relationship among congeners has been lacking (Floden, 2014; Chao and Tseng, 2019). Polygonatum falcatum A. Gray (Asparagaceae) is a perennial herb distributed in forest and forest margins of Japan and Korea (Tamura, 2016; Jang, 2018). Polygonatum falcatum has been widely used for oriental medicines and is well-known for its ornamental values (An et al., 2006; Tomioka et al., 2008). The species has recently drawn attention, as secondary metabolites extracted from its rhizome showed potential anti-adipogenic activities (Park et al., 2012).
Chloroplast genomes provide molecular markers that are a great tool for phylogenetic analyses from species to higher rank taxa (Gitzendanner et al., 2018). There is a growing number of studies resolving problematic relationships among taxa using a whole plastome (Martin et al., 2005; Gitzendanner et al., 2018). Many Polygonatum species have been recently studied for their plastome identity, however, the genomic information applicable for P. falcatum remains absent. In the present study, we investigated the genomic architecture of the whole chloroplast genome for P. falcatum using whole-genome shotgun sequencing.

MATERIALS AND METHODS

We collected young leaves of P. falcatum from Jeju-si, Korea (N 33°26′ 22.0″, E 126°37′ 46.0″). The voucher specimen was prepared and deposited at the Herbarium of Chosun University (CHO) with the accession number CHO0000063.
The total genomic DNA was extracted followed by the manufacturer’s protocol (QIAGEN, Hilden, Germany). After library preparation, the prepared libraries were sequenced on the Illumina HiSeq-X platform (Illumina, San Diego, CA, USA). Obtained reads were assembled with de novo strategy using Geneious Prime (ver. 2021.2.2) followed by Gibbs (2019). The genes were predicted with GeSeq (Tillich et al., 2017), and manually curated based on Blast search results. The simple sequence repeats were investigated with MISA with a default parameter setting (Beier et al., 2017). A circular map of the P. falcatum chloroplast genome was drawn by OGDRAW v. 1.3.1 (Greiner et al., 2019).
To investigate its phylogenetic relationship, the concatenated coding sequences from the entire chloroplast genome of 16 Polygonatum and outgroup taxa were aligned in MAFFT Online (Katoh et al, 2019). All sequences except P. falcatum were downloaded from NCBI GenBank. We assigned Heteropolygonatum as an outgroup following phylogenetic relationships based on a previous study (Floden and Schilling, 2018). We inferred the phylogeny using the maximum likelihood (ML) algorithm implemented in RAxML v. 4.0 with the GTR model with gamma rates (Stamatakis, 2006). For the clade support, 1,000 bootstrap replicates were used.

RESULTS AND DISCUSSION

We obtained 83 million high-quality 150 bp paired-end reads. A total of 12.6 Gb reads was assembled with de novo strategy. Assembled genome was 154,579 bp in length with the typical quadripartite structure comprising a large single-copy (LSC) (83,528 bp), a small single-copy (SSC) (18,457 bp), and a pair of inverted repeats (IRs) (26,297 bp) (Fig. 1). The overall GC content was 41.68%. The chloroplast genome contained 133 genes including 87 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Forty-seven simple sequence repeats were identified in the cp genome, most of which were mono-nucleotide repeats (Table 1). The complete chloroplast genome sequence of P. falcatum was deposited in GenBank with the accession number OM782296. The associated BioProject and Bio-Sample numbers are PRJNA809136 and SAMN26148647, respectively.
In our phylogenetic analysis based on the whole chloroplast genomes, 14 species of Polygonatum formed a monophyletic group (BP=100) with strong support on the ML tree (Fig. 2). The taxa that failed to form a monophyletic group in the ML tree (P. cyrtonema, P. odoratum, and P. verticillatum) are morphologically diverse and show broad distribution (Mehra and Pathania, 1960; Jeffrey, 1980; Floden and Schilling, 2018; Chen and Tamura, 2000). The result is somewhat consistent with the former phylogenetic studies which revealed high molecular variation that might in part be due to cryptic diversity unexplored (Meng et al., 2014; Floden and Schilling, 2018). The ML tree also indicated that P. falcatum is most closely related to P. odoratum (Fig. 2). Further study might be required to fully resolve the phylogenetic relationship within the genus.

Acknowledgments

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2021R1C1C1009176).

NOTES

CONFLICTS OF INTEREST
The authors declare that there are no conflicts of interest.

Fig. 1.
Chloroplast genome annotations of a Polygonatum falcatum drawn by OGDRAW v. 1.3.1.
kjpt-52-1-80f1.jpg
Fig. 2.
Maximum-likelihood (ML) tree based on chloroplast genome sequences of 14 species of Polygonatum. Numbers on the nodes indicated the bootstrap support value (>50%).
kjpt-52-1-80f2.jpg
Table 1.
Summary of simple sequence repeats (SSRs) across varying unit sizes in P. falcatum.
Unit size Number of SSRs
1 42
2 4
3 1

LITERATURE CITED

An, SM. Ryuk, JA. Kim, YH. Chae, BC. Kim, HJ. Kim, KH. Kang, KK. Ko, BS and Lee, MY. 2006. Genetic analysis of Polygonati rhizoma and Polygonati odorati rhizoma using random amplified microsatellite polymorphism. Korean Journal of Medicinal Crop Science 14: 125-129 (in Korean).

Beier, S. Thiel, T. Münch, T. Scholz, U and Mascher, M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics 33: 2583-2585.
crossref
Chen, XQ and Tamura, MN. 2000. Polygonatum. In Flora of China. 24: Flagellariaceae through Marantaceae. Wu, ZW. Raven, PH (eds.), Science Press, Beijing and Missouri Botanical Garden Press, St Louis, MP. Pp. 225-235.

Floden, A. 2017. Molecular phylogenetic studies of the genera of tribe Polygonateae (Asparagaceae: Nolinoideae): Disporopsis, Heteropolygonatum, and Polygonatum . PhD dissertation,. University of Tennessee; Knoxville.

Floden, A and Schilling, EE. 2018. Using phylogenomics to reconstruct phylogenetic relationships within tribe Polygonateae (Asparagaceae), with a special focus onPolygonatum . Molecular Phylogenetics and Evolution 129: 202-213.
crossref
Gibbs, MD. 2019. De novo assembly and reconstruction of complete circular chloroplast genomes using Geneious Prime. Biomatters https://assets.geneious.com/documentation/geneious/App+Note+-+De+Novo+Assembly+of+Chloroplasts.pdf .

Gitzendanner, MA. Soltis, PS. Yi, TS. Li, DZ and Soltis, DE. 2018. Plastome phylogenetics: 30 years of inferences into plant evolution. Advances in Botanical Research. Chaw, SM. Jansen, RK (eds.), Academic Press, London. Pp. 293-313.
crossref
Jang, CG. 2018. Polygonatum . The Genera of Vascular Plants of Korea. Flora of Korea Editorial Committee (ed.), Hongreung Publishing Company, Seoul. Pp. 1747-1753 (in Korean).

Jeffrey, C. 1980. The genus Polygonatum (Liliaceae) in eastern Asia. Kew Bulletin 34: 435-471.

Katoh, K. Rozewicki, J and Yamada, KD. 2019. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20: 1160-1166.
crossref
Kim, JH. Seo, JW. Byeon, JH. Ahn, YS. Chaand, SW and Cho, JH. 2014. Morphological characteristics and phylogenetic analysis of Polygonatum species based on chloroplast DNA sequences. Korean Journal of Medicinal Crop Science 22: 489-496 (in Korean).
crossref
Lee, SY. Chen, Z. Chen, Z. Chen, J. Zhang, X. Pan, J. Fan, Q and Liao, W. 2021. Plastid genome sequencing, identification of nuclear SNP markers, and quality assessment of medicinal rhizomatous herb Polygonatum odoratum (Asparagaceae) cultivars. Ecology and Evolution 11: 7660-7676.
crossref
Martin, W. Deusch, O. Stawski, N. Grünheit, N and Goremykin, V. 2005. Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution. Trends in Plant Science 10: 203-209.
crossref
Mehra, PN and Pathania, RS. 1960. A cytotaxonomic study of the West Himalayan Polygonatum . Cytologia 25: 179-194.
crossref
Meng, Y. Nie, ZL. Deng, T and Wen, J. 2014. Phylogenetics and evolution of phyllotaxy in the Solomon’s seal genus Polygonatum (Asparagaceae: Polygonateae). Botanical Journal of the Linnean Society 176: 435-451.
crossref
Park, UH. Jeong, JC. Jang, JS. Sung, MR. Youn, HS. Lee, SJ. Kim, EJ and Um, SJ. 2012. Negative regulation of adipogenesis by kaempferol, a component of rhizoma Polygonati falcatum in 3T3-L1 Cells. Biological and Pharmaceutical Bulletin 35: 1525-1533.
crossref
Tamura, MN. 2016. Polygonatum . Flora of Japan. IVb: Iwatsuki, K. Boufford, DE. Ohba, H (eds.), Kodansha, Tokyo. Pp. 152-158.

Tillich, M. Lehwark, P. Pellizzer, T. Ulbricht-Jones, ES. Fischer, A. Bock, R and Greiner, S. 2017. GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Res 45: W6-W11.

Tomioka, K. Moriwaki, J and Sato, T. 2008. Anthracnose of Polygonatum falcatum caused by Colletotrichum dematium . Journal of General Plant Pathology 74: 402-404.

Zhao, P. Zhao, C. Li, X. Gao, Q. Huang, L. Xiao, P and Gao, W. 2018. The genus Polygonatum: A review of ethnopharmacology, phytochemistry and pharmacology. Journal of ethnopharmacology 214: 274-291.
crossref
Editorial Office
Korean Journal of Plant Taxonomy
Department of Biology, Daejeon University, Daejeon 34520, Korea
TEL: +82-42-280-2434   E-mail: kjpt1968@gmail.com
About |  Browse Articles |  Current Issue |  For Authors and Reviewers
Copyright © Korean Society of Plant Taxonomists.                 Developed in M2PI