Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong”
Abstract
:1. Introduction
2. Results
2.1. Six Complete Cp Genomes and 45S Nrdna Sequences of Three Apiaceae Species
2.2. Identification of Intraspecies Variations within Three Apiaceae Cp Genomes
2.3. IR Expansion and Structural Variations among Three Apiaceae Species
2.4. Tandem Repeats and Copy Number Variations in the Cp Genomes of Three Species
2.5. Sequence Variations of 45S DNA Sequences of Three Species
2.6. Phylogenetic Analysis and Divergence Time Estimation
2.7. Comparison of Mutation Rate among All Cp Protein-Coding Genes in the Three Apiaceae Species
2.8. Development of Barcode Markers Derived from cp Genomes and 45S nrDNA Sequences
3. Discussion
3.1. Molecular Phylogeny of the Apiaceae Species
3.2. Intraspecies Chloroplast Variation and DNA Barcoding Markers for Species Authentication
3.3. Unique Structural Changes in the cp Genome of P. japonicum
3.4. Variation in the cp Genomes and 45S nrDNA of Three Species
3.5. Cp Gene Selection Pressure and Phylogenetic Relationship of Three Apiaceae Species
4. Materials and Methods
4.1. Plant Materials
4.2. Genomic DNA Preparation and Whole-Genome Shotgun Sequencing
4.3. Cp Genome and 45S nrDNA Assembly
4.4. Gene and Structural Annotation
4.5. Comparative Sequence Analysis at the Intraspecies and Interspecies Level
4.6. Development and Validation of DNA Barcode Markers
4.7. Calculation of Nucleotide Substitution Value
4.8. Phylogenetic Analysis
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Species (Common Name in Traditional Korean Medicine) | Accession | Raw Data (Gbp) | Chloroplast Genome | 45S nrDNA | ||||
---|---|---|---|---|---|---|---|---|
Length (bp) | Coverage (x) d | GenBank Accession No. (Reference) | Length (bp) e | Coverage (x) d | GenBank Accession No. (Reference) | |||
Ledebouriella seseloides (Bang-poong) | Ls-01 a | 1.67 | 147,880 | 255.15 | KT153021 (Lee et al., 2015a) | 5815 | 659.94 | KX757774 (This study) |
Ls-02 b | 5.05 | 147,830 | 177.95 | KU866529 (This study) | 5815 | 2550.62 | KX757775 (This study) | |
Peucedanum japonicum (Sik-bang-poong) | Pj-01 a | 2.08 | 164,653 | 369.41 | KU866530 (This study) | 5815 | 943.43 | KX757776 (This study) |
Pj-02 b | 5.18 | 164,653 | 945.25 | KU866531 (This study) | 5815 | 2418.35 | KX757777 (This study) | |
Glehnia littoralis (Hae-bang-poong) | Gl-01 c | 1.06 | 147,467 | 146.53 | KT153022 (Lee et al., 2015b) | 5812 | 399.28 | KX757778 (This study) |
Gl-02 b | 4.72 | 147,477 | 367.41 | KU866532 (This study) | 5812 | 1638.57 | KX757779 (This study) |
No. | TR Unit Sequence | Unit Length (bp) | Copy Number | Position | ||
---|---|---|---|---|---|---|
Ls | Pj | Gl | ||||
1 | AATAAGTAACTAG | 13 | 2 | 1 | 1 | trnK-UUU ~ rps16 |
2 | TTCTTCTATACAAA | 14 | 2 | 2 | 2 | rps16 ~ trnQ-UUG |
3 | AAAGATATGATTCATA | 16 | 2 | 2 | 1 | rps16 ~ trnQ-UUG |
4 | TAAAAAATATAAA | 13 | 2 | 1 | 1 | atpF ~ atpH |
5 | AGGAATCATTAAA | 13 | 2 | 1 | 1 | rps2 ~ rpoC2 |
6 | TATATTGTTATAAT | 14 | 1 | 1 | 2 | rpoB ~ trnC-GCA |
7 | TATAATATTAATAAG | 15 | 2 | nf | nf | trnE-UUC ~ trnT-GGU |
8 | TATATAGGAAGTATGAT | 17 | nf | 2 | 1 | trnS-UGA ~ lhbA |
9 | ATCTAGATAAGATTTATA | 18 | 2 | 1 | 1 | trnM-CAU ~ psbD |
10 | TTAAATGGTATTTATTAAT | 19 | 2 | 1 | 1 | trnS-UGA ~ lhbA |
11 | ATTAGCCATTACTAATAG | 18 | 1 | 2 | 1 | psaA ~ ycf3 |
12 | TAACCTAAGTGCAAAAATAGA | 21 | 1 | 2 | 1 | ycf3 ~ trnS-GGA |
13 | TATTCTATATATATATATTCTATATA | 26 | 1 | 2 | 1 | rps4 ~ trnT-UGU |
14 | TTTATATATATATATAT | 17 | 2 | 1 | 1 | ndhC ~ trnV-UAC |
15 | TTATCTTTATAATTTAA | 18 | 1 | 2 | 1 | accD ~ psaI |
16 | TATATGTATATTGA | 14 | 2 | 2 | 1 | psaI ~ ycf4 |
17 | TTATTCCAGTAAAA | 14 | 2 | 2 | 2 | cemA ~ petA |
18 | AAGGAAGTACTC | 12 | 1 | 2 | 1 | psbE ~ petL |
19 | ATTATATATAT | 11 | nf | 3 | 1 | trnW-CCA ~ trnP-UGG |
20 | TTATACAAGGTACTTAAATGTAAA | 24 | 2 | 1 | 1 | psaJ ~ rpl33 |
21 | TTCTATATAGAACATAATTAAATA | 24 | 2 | 2 | 2 | rpl33 ~ rps18 |
22 | TAAAGTTCCAACTAAAAAG | 19 | 2 | 1 | 2 | psbT ~ psbN |
23 | TCCCCTTTTT | 10 | 1 | 2 | 1 | rps11 ~ rpl36 |
24 | ATATTTTTAAATTG | 14 | 2 | 2 | 3 | rpl16 ~ rps3 |
25 | TCTTATAGAATTAGAATTGT | 20 | 2 | 1 | 1 | rpl16 ~ rps3 |
26 | CCTATTGCCGATACA | 15 | 2 | 2 | 2 | ycf2 |
27 | TAGTGACGATATTGATGC | 18 | 6/5 a | 4 | 3 | ycf2 (marker ID CNV01) |
28 | AAACTCTCTTCAAGAGTTATTAACACCAACCCGGTGTTC | 39 | nf | 2 | nf | ycf2 ~ trnL-CAA |
29 | TGGTGGAGATCAGAAAGAGAA | 21 | 2 | 1 | nf | ycf2 ~ trnL-CAA |
30 | TGTAATGTACTT | 12 | 2 | 1 | 1 | ycf2 ~ trnL-CAA |
31 | TCTTTTCTTCCGTGATGAACT | 21 | 3 | 1 | 1 | ycf15 |
32 | ACCGAAAGGAAAAGCGTGAA | 20 | 2 | 2 | 3 | trnI-GAU ~ trnI-GAU |
33 | CATTGTTCAACTCTTTGACAACACGAAAAAAC | 32 | 2 | 2 | 2 | rrn4.5 ~ rrn5 |
34 | AAAAAGAAATAAAT | 14 | 2 | 2 | 1 | trnR-ACG |
35 | TTCTATTTCTTTTCTATATATG | 22 | 1 | 4 | 1 | trnN-GUU ~ ycf1 (marker ID CNV02) |
36 | TATTAATATTAATAAAT | 17 | 2 | nf | nf | ycf1 ~ ndhF |
37 | TATATATGTATAAA | 14 | 2 | nf | nf | rpl32 ~ trnL-UAG |
38 | AAATATTAATCTACTTCT | 18 | 2 | 1 | 1 | psaC ~ ndhE (marker ID CNV03) |
39 | TTATGAATATAA | 12 | 2 | 2 | 2 | psaC ~ ndhE |
40 | TATTATTTTTTATTA | 15 | 2 | 1 | 1 | ndhA ~ orf188 |
Marker ID | Primer Sequence (5′–3′) | Product Size a | Location |
---|---|---|---|
Ls/Pj/Gl (bp) | |||
CNV01 | F: GGTCAAATACCTAGCGACAA | 308/272/254 | ycf2 |
R: TTATGCAAGGAGACATTGCT | |||
CNV02 | F: CATCCATATCCCAATTCCAT | 305/371/305 | trnN-GUU ~ ycf1 |
R: GCTCGGAGAAGGAAGAGATA | |||
CNV03 | F: CATTGAGTGCACCCTATACA | 404/386/368 | psaC ~ ndhE |
R: TCGTAACAGAAAATCAACTCG | |||
InDel01 | F: AACGAATCCTACGGTTTCTC | 266/289/269 | trnS-GCU ~ trnR-UCU |
R: TGTCGAACAGGGATAATTTG | |||
InDel02 | F: TCTCGCTTTTTAGTCAGTTTG | 380/379/416 | ndhF ~ rpl32 |
R: GCCTAATGAAAAGCCTAATGA | |||
InDel03 | F: CAGGAGGATAGCAAGTTACAA | 412/571/571 | rps12 ~ trnV-GAC |
R: CAACGCCACTATTCTTGAAC | |||
InDel04 | F: CTATATGTATATACAATAACGAATCA | 652/198/633 | trnE-UUC ~ trnT-GGU |
R: GTTCAAGAATAGTGGCGTTG | |||
IR01 | LSC P: CCTAGCTGCTGTTGAAGCTC | na/576/na | psbA |
Control F: GACGACTGAGCCAACTTGAT | 262/262/262 | psbH ~ petB | |
Control R: TCGAGACGTTCTTCAAACCA | |||
nrDNA01 | Specific F: GTTAACAATTAGGGCGAGCA | na/na/291 | ITS1 |
Control F: GCATCGATGAAGAACGTAGC | 78/78/78 | 5.8S | |
Control R: GCGTTCAAAGACTCGATGGT |
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Lee, H.O.; Joh, H.J.; Kim, K.; Lee, S.-C.; Kim, N.-H.; Park, J.Y.; Park, H.-S.; Park, M.-S.; Kim, S.; Kwak, M.; et al. Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong”. Int. J. Mol. Sci. 2019, 20, 2196. https://doi.org/10.3390/ijms20092196
Lee HO, Joh HJ, Kim K, Lee S-C, Kim N-H, Park JY, Park H-S, Park M-S, Kim S, Kwak M, et al. Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong”. International Journal of Molecular Sciences. 2019; 20(9):2196. https://doi.org/10.3390/ijms20092196
Chicago/Turabian StyleLee, Hyun Oh, Ho Jun Joh, Kyunghee Kim, Sang-Choon Lee, Nam-Hoon Kim, Jee Young Park, Hyun-Seung Park, Mi-So Park, Soonok Kim, Myounghai Kwak, and et al. 2019. "Dynamic Chloroplast Genome Rearrangement and DNA Barcoding for Three Apiaceae Species Known as the Medicinal Herb “Bang-Poong”" International Journal of Molecular Sciences 20, no. 9: 2196. https://doi.org/10.3390/ijms20092196