Deciphering the Plastome and Molecular Identities of Six Medicinal “Doukou” Species
Abstract
:1. Introduction
2. Results
2.1. Plastome Structural Variation, Sequence Divergences, and Hypervariable Regions
2.2. Sequence Characteristics
2.3. Distance Based Species Discrimination
2.4. Tree Based Species Discrimination
3. Discussion
3.1. Plastome Characteristics and DNA Barcode Performance
3.2. Performance Comparison of Species Delimitation Methods
3.3. DNA Barcoding in Six Medicinal “Doukou” Plants
3.4. NCBI Database as a Resource and ITS vs. ITS1 Identification Rate
4. Materials and Methods
4.1. Taxon Sampling
4.2. DNA Extraction, Sequencing, Assembly, and Annotation
4.3. Data Analysis
4.3.1. Plastome Structural Variation, Divergence, and Mutational Hotspot Analyses
4.3.2. Sequence-Based Analyses
4.3.3. Phylogenetic Tree-Based Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Dataset | No. of Samples | Aligned Length (bp) | No. of Variable Sites (% Divergence) | No. of Parsimony Informative Sites (% Divergence) | GC Content (%) | No. of Conserved Sites (% Divergence) | No. of Singleton Sites (% Divergence) |
---|---|---|---|---|---|---|---|
ITS | 65 | 609 | 164 (26.9) | 120 (19.7) | 56.2 | 422 (69.3) | 42 (6.9) |
ITS1 | 65 | 194 | 70 (36.1) | 59 (30.4) | 56.5 | 111 (57.2) | 11 (5.7) |
ITS2 | 65 | 222 | 83 (37.4) | 58 (26.1) | 60.1 | 130 (58.6) | 23 (10.4) |
Complete plastomes | 44 | 168,519 | 5299 (3.1) | 3280 (1.9) | 36.1 | 161,202 (95.7) | 1980 (1.2) |
matK | 82 | 716 | 44 (6.1) | 28 (3.9) | 28.7 | 672 (93.9) | 16 (2.2) |
rbcL | 61 | 490 | 12 (2.4) | 9 (1.8) | 43.2 | 478 (97.6) | 3 (0.6) |
psbA-trnH | 66 | 804 | 65 (8.1) | 35 (4.4) | 29.2 | 690 (85.8) | 30 (3.7) |
ycf1 | 44 | 7090 | 162 (2.3) | 91 (1.3) | 30.9 | 6832 (96.4) | 67 (0.9) |
Sample Number | Species | Country | Province | Region | Locality | GenBank Accession Numbers for Each DNA Region | |
---|---|---|---|---|---|---|---|
ITS/ITS1/ITS2 | CP/matK/rbcL/psbA-trnH | ||||||
YWB91902-1 | Wurfbainia compacta | China | Yunnan | Xishuangbanna Dai Autonomous Prefecture | Mengla County | OR801269 | PP826179 |
YWB91902-2 | Wurfbainia compacta | China | Yunnan | Xishuangbanna Dai Autonomous Prefecture | Mengla County | OR801270 | PP826180 |
YWB91901-1 | Wurfbainia vera | China | Yunnan | Xishuangbanna Dai Autonomous Prefecture | Mengla County | OR801267 | PP826177 |
YWB91901-2 | Wurfbainia vera | China | Yunnan | Xishuangbanna Dai Autonomous Prefecture | Mengla County | OR801268 | PP826178 |
S07964 | Lanxangia paratsaoko | China | Yunnan | Honghe Hani and Yi Autonomous Prefecture | Yuanyang County | OR801266 | PP826176 |
S00918 | Wurfbainia villosa | China | Guangxi | Fangchengang City | Shangsi County | OR801265 | PP826175 |
B190333 | Wurfbainia villosa | China | Yunnan | Kunming City | Xishan District | OR801256 | PP826171 |
B190623 | Wurfbainia villosa | China | Yunnan | Kunming City | Xishan District | OR801257 | PP826172 |
B190641 | Wurfbainia villosa | China | Yunnan | Kunming City | Xishan District | OR801258 | PP826173 |
YWS1-25-1 | Wurfbainia villosa | China | Yunnan | Xishuangbanna Dai Autonomous Prefecture | Mengla County | OR801271 | PP826181 |
YWS1-25-5 | Wurfbainia villosa | China | Yunnan | Xishuangbanna Dai Autonomous Prefecture | Jinghong City | OR801272 | PP853448 |
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Zhao, Y.; Kipkoech, A.; Li, Z.-P.; Xu, L.; Yang, J.-B. Deciphering the Plastome and Molecular Identities of Six Medicinal “Doukou” Species. Int. J. Mol. Sci. 2024, 25, 9005. https://doi.org/10.3390/ijms25169005
Zhao Y, Kipkoech A, Li Z-P, Xu L, Yang J-B. Deciphering the Plastome and Molecular Identities of Six Medicinal “Doukou” Species. International Journal of Molecular Sciences. 2024; 25(16):9005. https://doi.org/10.3390/ijms25169005
Chicago/Turabian StyleZhao, Ying, Amos Kipkoech, Zhi-Peng Li, Ling Xu, and Jun-Bo Yang. 2024. "Deciphering the Plastome and Molecular Identities of Six Medicinal “Doukou” Species" International Journal of Molecular Sciences 25, no. 16: 9005. https://doi.org/10.3390/ijms25169005