Authentication of Herbal Medicines Dipsacus asper and Phlomoides umbrosa Using DNA Barcodes, Chloroplast Genome, and Sequence Characterized Amplified Region (SCAR) Marker
Abstract
:1. Introduction
2. Results and Discussion
2.1. Authentication of D. asper, D. japonicus, and P. umbrosa Using DNA Barcodes
2.2. CP Genome Organisation of D. asper and D. japonicus
2.3. Analysis of Repeats in the CP Genomes of D. asper and D. japonicus
2.4. Comparative Analysis of CP Genomes within Caprifoliaceae
2.5. Authentication of D. asper, D. japonicus, and P. umbrosa Using SCAR Markers
3. Materials and Methods
3.1. Plant Materials
3.2. Universal DNA Barcode Analysis for D. asper, D. japonicus, and P. umbrosa
3.3. Genome Sequencing and Assembly
3.4. Genome Annotation and Comparative Analysis
3.5. Repeat Analysis
3.6. Phylogenetic Analysis
3.7. Development of SCAR Markers for D. asper, D. japonicus, and P. umbrosa
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample Availability: Samples of D. asper, D. japonicus, and P. umbrosa are available from the authors and the herbarium of KIOM. |
Species | DNA | AL 1 Length (bp) | Parsimony Informative Sites | Variable Sites | Nucleotide Diversity (Pi) | No. of Indels | No. of Haplotypes | ||
---|---|---|---|---|---|---|---|---|---|
No. | % | No. | % | ||||||
D. asper vs. D. japonicus vs. P. umbrosa | ITS2 | 390 | 91 | 23.3 | 145 | 37.2 | 0.12842 | 8 | 8 |
matK | 1276 | 234 | 18.3 | 242 | 19.0 | 0.10377 | 2 | 8 | |
rbcL | 1511 | 106 | 7.0 | 113 | 7.5 | 0.0394 | 1 | 6 | |
D. asper vs. D. japonicus | ITS2 | 379 | 7 | 1.8 | 9 | 2.4 | 0.00718 | 0 | 4 |
matK | 1264 | 5 | 0.4 | 8 | 0.6 | 0.00332 | 0 | 4 | |
rbcL | 1501 | 3 | 0.2 | 6 | 0.4 | 0.00233 | 0 | 4 |
Characteristic | D. asper | D. japonicus |
---|---|---|
Accession number | MH074864 | MH074865 |
Total CP genome size (bp) | 160,530 | 160,371 |
LSC region (bp) | 86,979 | 87,193 |
IR region (bp) | 27,821 | 27,664 |
SSC region (bp) | 17,909 | 17,850 |
Number of genes | 112 | 112 |
Protein-coding genes | 79 | 79 |
rRNA | 4 | 4 |
tRNA | 29 | 29 |
Introns (bp) | 14,368 | 14,392 |
Intergenic spacers (bp) | 50,578 | 51,526 |
GC content (%) | 38.8 | 38.8 |
LSC (%) | 37.2 | 37.1 |
IR (%) | 42.8 | 42.9 |
SSC (%) | 34.2 | 34.2 |
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Park, I.; Yang, S.; Kim, W.J.; Noh, P.; Lee, H.O.; Moon, B.C. Authentication of Herbal Medicines Dipsacus asper and Phlomoides umbrosa Using DNA Barcodes, Chloroplast Genome, and Sequence Characterized Amplified Region (SCAR) Marker. Molecules 2018, 23, 1748. https://doi.org/10.3390/molecules23071748
Park I, Yang S, Kim WJ, Noh P, Lee HO, Moon BC. Authentication of Herbal Medicines Dipsacus asper and Phlomoides umbrosa Using DNA Barcodes, Chloroplast Genome, and Sequence Characterized Amplified Region (SCAR) Marker. Molecules. 2018; 23(7):1748. https://doi.org/10.3390/molecules23071748
Chicago/Turabian StylePark, Inkyu, Sungyu Yang, Wook Jin Kim, Pureum Noh, Hyun Oh Lee, and Byeong Cheol Moon. 2018. "Authentication of Herbal Medicines Dipsacus asper and Phlomoides umbrosa Using DNA Barcodes, Chloroplast Genome, and Sequence Characterized Amplified Region (SCAR) Marker" Molecules 23, no. 7: 1748. https://doi.org/10.3390/molecules23071748