https://orcid.org/0000-0002-9206-4874
Abstract
In this study, we sequenced the complete chloroplast genome of Polygonatum odoratum with Illumina sequencing technology. The complete chloroplast genome length is 156,082 bp shows a typical tetrad structure, which manifests as one large and one small single copy (LSC and SSC) regions of 85,009 and 18,513 bp, isolated by two inverted repeat regions (IRs) of 26,280 bp. This study annotated altogether 131 unique genes, consisting of 86 protein-encoding genes, 8 rRNA, and 38 tRNA. According to the maximum likelihood phylogenetic tree based on eight complete chloroplast genomes, P. odoratum shows a close association with additional Maianthemum genus. The chloroplast genome-wide for P. odoratum would help to conserve the precious natural populations.
Polygonatum odoratum (Mill.) Druce, a typical representative of the Liliaceae family, is a perennial herbaceous plant that is widely distributed in East Asia and Europe (Zhao et al. Citation2018). Polygonatum odoratum has been found to contain several components with bioactive effects, including polysaccharides, steroidal glycosides, dipeptides, flavonoids, amino acids, and trace mineral elements (Lin et al. Citation1994; Deng et al. Citation2012). Polygonatum odoratum rhizomes are regarded as the medicinal parts of the plant, and have been used extensively to treat diseases such as rheumatic heart disease, hypoimmunity, cardiovascular diseases, and diabetes (China Pharmacopoeia Committee Citation2015). Polygonatum odoratum has been recognized as the endemic medicinal perennial herb, because resources of this herb are diminishing due to uncontrolled harvesting. Therefore, it is necessary for us to learn more about its genetic data and pay more attention to it. Notably, the chloroplast genome-wide for P. odoratum would help to conserve the precious natural populations.
In this study, silica-gel-dried leaves of P. odoratum were collected from Xianggelila of Yunnan Province, China (99°39.844E, 27°53.684N), and voucher specimens (PO201909001) were deposited in the Herbarium of Yunnan University of Chinese Medicine. Genomic DNA was extracted with the CTAB method (Doyle and Doyle Citation1987). For Illumina sequencing, at least 2 μg genomic DNA was used for each sample in sequencing library construction. Paired-end libraries with the insert size of 400 bp were constructed according to the manufacturer’s instructions (Biooscientific, AIR™ Paired-End DNA Sequencing Kit, Austin, TX) and then sequenced on Illumina Hiseq X-Ten (Illumina, San Diego, CA). There are 2.16 GB of sequence data was generated. The reads of the complete chloroplast genome were assembled using de novo assembling constructed in SPAdes version 3.9.1 (Bankevich et al. Citation2012), using kmer lengths of 21–105 bp; followed by reference guided assembling conducted with Bandage version 0.8.1 (Wick et al. Citation2015) and Geneious version 9.1.4 (Kearse et al. Citation2012). Polygonatum humile (GenBank: MN218691) was used as reference for annotation using GeSeq (Tillich et al. Citation2017), coupled with manual correction for boundaries.
The complete chloroplast genome of P. odoratum was 156,082 bp in length (GenBank accession number: MT646047), the GC content was 37.7%. Large single-copy (LSC) and small single-copy (SSC) regions contained 85,009 and 18,513 bp, respectively, while inverted repeat regions (IR) was 26,280 bp in length. A total of 131 unique genes were annotated, including 38tRNA, 8rRNA, and 85 protein-coding genes. Seven protein-coding genes, nine tRNA, and four rRNA genes were duplicated in the IR regions. In total, 18 intron-containing genes were in the chloroplast genome of P. odoratum of which three genes (rps12, clpP, and ycf3) include two introns and the rest include a single intron.
Six complete chloroplast genome sequences of Polygonatum and one complete chloroplast genome sequences of Maianthemun were downloaded from NCBI to further investigate the phylogenetic position of P. odoratum. We constructed a maximum likelihood tree using RAxML (Stamatakis Citation2014) after the sequences were aligned using MAFFT (Katoh and Standley Citation2013). The best nucleotide substitution model for constructing the phylogenetic tree is the Tamura–Nei model. Phylogenetic trees show that the species of Polygonatum were clustered into one branch and formed a monophyletic clade with 100% bootstrap support value (). The cladistic clustering of P. odoratum and P. odoratum was close and had high support rate. The complete chloroplast genome of P. odoratum would help in understanding the genetic information and conserving the precious natural populations.
Figure 1. Maximum likelihood phylogenetic tree based on eight complete chloroplast genomes (bootstrap repeat is 1000).
Disclosure statement
No potential conflict of interest was reported by the author(s).
Data availability statement
The data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov, reference number MT646047.
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References
- Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477.
- China Pharmacopoeia Committee. 2015. Drug standard of ministry of public health of the people s republic of China. Beijing, China: People’s Medical Publishing House.
- Deng Y, He K, Ye X, Chen X, Huang J, Li X, Yuan L, Jin Y, Jin Q, Li P. 2012. Saponin rich fractions from Polygonatum odoratum (Mill.) Druce with more potential hypoglycemic effects. J Ethnopharmacol. 141(1):228–233.
- Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytoch Bull. 19:11–15.
- Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780.
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, et al. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 28(12):1647–1649.
- Lin HW, Han GY, Liao SX. 1994. Studies on the active constituents of the Chinese traditional medicine Polygonatum odoratum (Mill.) Druce. Yao xue xue bao. Acta Pharm Sin. 29(3):215–222.
- Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30(9):1312–1313.
- Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S. 2017. GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45:6–11.
- Wick RR, Schultz MB, Zobel J, Holt KE. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 31(20):3350–3352.
- Zhao P, Zhao C, Li X, Gao Q, Huang L, Xiao P, Gao W. 2018. The genus Polygonatum: a review of ethnopharmacology, phytochemistry and pharmacology. J Ethnopharmacol. 214:274–291.