Accurate authentication of Dendrobium officinale and its closely related species by comparative analysis of complete plastomes
| Autor: | Zhitao Niu, Xiaoyu Ding, Shuying Zhu, Qingyun Xue, Xuezhu Xie, Hui Wang |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Original article Inverted repeat CE capillary electrophoresis Biology Intraspecific competition HPLC high-pressure liquid chromatography Dendrobium Discriminatory power 03 medical and health sciences Dendrobium officinale Indels insertions/deletions LSC large single copy region SSC small single copy region Plastomic comparison General Pharmacology Toxicology and Pharmaceutics Genetic marker Gene Complete plastome sequence Authentication lcsh:RM1-950 SV sequence variability IR inverted repeat region biology.organism_classification ML maximum likelihood NGS next-generation sequencing lcsh:Therapeutics. Pharmacology 030104 developmental biology Chloroplast DNA Evolutionary biology SNPs single nucleotide polymorphisms BS bootstrap value |
| Zdroj: | Acta Pharmaceutica Sinica. B Acta Pharmaceutica Sinica B, Vol 8, Iss 6, Pp 969-980 (2018) |
| ISSN: | 2211-3835 |
| Popis: | Owing to its great medicinal and ornamental values, Dendrobium officinale is frequently adulterated with other Dendrobium species on the market. Unfortunately, the utilization of the common DNA markers ITS, ITS2, and matK+rbcL is unable to distinguish D. officinale from 5 closely related species of it (D. tosaense, D. shixingense, D. flexicaule, D. scoriarum and D. aduncum). Here, we compared 63 Dendrobium plastomes comprising 40 newly sequenced plastomes of the 6 species and 23 previously published plastomes. The plastomes of D. officinale and its closely related species were shown to have conserved genome structure and gene content. Comparative analyses revealed that small single copy region contained higher variation than large single copy and inverted repeat regions, which was mainly attributed to the loss/retention of ndh genes. Furthermore, the intraspecific sequence variability among different Dendrobium species was shown to be diversified, which necessitates a cautious evaluation of genetic markers specific for different Dendrobium species. By evaluating the maximum likelihood trees inferred from different datasets, we found that the complete plastome sequence dataset had the highest discriminatory power for D. officinale and its closely related species, indicating that complete plastome sequences can be used to accurately authenticate Dendrobium species. Graphical abstract In this study, the authors compared 63 Dendrobium plastomes comprising 40 newly sequenced plastomes of this group and 23 previously published plastomes. By evaluating the maximum likelihood (ML) trees inferred from different sequence datasets, we found that D. officinale and its closely related species could be accurately authenticated by using the complete plastome sequences.fx1 |
| Databáze: | OpenAIRE |
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