The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species
Abstract
:1. Introduction
2. Materials and Methods
2.1. Genome Sequencing and Assembly
2.2. Genome Annotation and Comparative Analysis
2.3. Repeat Analysis
2.4. Phylogenic and Divergence Analysis
3. Results
3.1. Chloroplast Genome Organization of Two Fritillaria Species
3.2. Repeat Analysis in Two Fritillaria Chloroplast Genomes
3.3. Comparison of the Chloroplast Genomes with Those of Other Fritillaria Species
3.4. Phylogenic Analysis
4. Discussion
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
CP | Chloroplast |
LSC | Large Single Copy |
SSC | Small Single Copy |
IR | Inverted Repeat |
tRNA | Transfer RNA |
rRNA | Ribosomal RNA |
NGS | Next-Generation Sequencing |
KIOM | Korea Institute of Oriental Medicine |
ML | Maximum Likelihood |
MP | Maximum Parsimony |
WGS | Whole-Genome Sequencing |
IRb | Inverted Repeat b |
SSRs | Simple Sequence Repeats |
SNPs | Single-Nucleotide Polymorphisms |
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Sample Availability: Not available. |
Species | Fritillaria ussuriensis | Fritillaria cirrhosa |
---|---|---|
Total CP genome size (bp) | 151,524 | 151,083 |
LSC (bp) | 81,732 | 81,390 |
IR (bp) | 52,678 | 52,156 |
SSC (bp) | 17,114 | 17,537 |
GC content (%) | 36.95 | 36.96 |
LSC (%) | 34.71 | 34.79 |
IR (%) | 42.40 | 42.60 |
SSC (%) | 30.63 | 30.50 |
Total number of genes | 111 | 112 |
Protein-coding gene | 77 | 78 |
rRNA | 4 | 4 |
tRNA | 30 | 30 |
Gene Products of Two Fritillaria Species | |
---|---|
Photosystem I | psaA, B, C, I, J |
Photosystem II | psbA, B, C, D, E, F, H, I, J, K, L, M, N, T, Z |
Cytochrome b6/f | petA, B (1), D (1), G, L, N |
ATP synthase | atpA, B, E, F (1), H, I |
Rubisco | rbcL |
NADH oxidoreductase | ndhA (1), B (1,3), C, D, E, F, G, H, I, J, K |
Large subunit ribosomal proteins | rpl2 (1,3), 14, 16 (1), 20, 22, 23 (3), 32, 33, 36 |
Small subunit ribosomal proteins | rps2, 3, 4, 73 (3), 8, 11, 12 (2–4), 14, 15, 16, 18, 19 |
RNA polymerase | rpoA, B, C1 (1), C2 |
Unknown function protein-coding gene | ycf1 (3), 2 (3), 3 (2), 4 |
Other genes | accD, ccsA, cemA (5), clpP (2), matK |
Ribosomal RNAs | rrn16 (3), 23 (3), 4.5 (3), 5 (3) |
Transfer RNAs | trnA-UGC (1,3), trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-UCC (1), trnG-GCC, trnH-GUG, trnI-CAU (3), trnI-GAU (1,3), trnK-UUU1 (3), trnL-UAA1 (3), trnL-UAG, trnL-CAA (3), trnM-CAU, trnfM-CAU, trnN-GUU (3), trnP-UGG, trnQ-UUG, trnR-ACG (3), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-UAC (1), trnV-GAC (3), trnW-CCA, trnY-GUA |
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Park, I.; Kim, W.J.; Yeo, S.-M.; Choi, G.; Kang, Y.-M.; Piao, R.; Moon, B.C. The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species. Molecules 2017, 22, 982. https://doi.org/10.3390/molecules22060982
Park I, Kim WJ, Yeo S-M, Choi G, Kang Y-M, Piao R, Moon BC. The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species. Molecules. 2017; 22(6):982. https://doi.org/10.3390/molecules22060982
Chicago/Turabian StylePark, Inkyu, Wook Jin Kim, Sang-Min Yeo, Goya Choi, Young-Min Kang, Renzhe Piao, and Byeong Cheol Moon. 2017. "The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species" Molecules 22, no. 6: 982. https://doi.org/10.3390/molecules22060982