The Complete Chloroplast Genomes of Two Lancea Species with Comparative Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. DNA Extraction and Sequencing
2.2. Chloroplast Genome Assembly and Annotation
2.3. Repeat Structure Analysis
2.4. Genome Comparison
2.5. Phylogenetic Analysis
3. Results
3.1. Characteristics of the Chloroplast Genomes
3.2. Repeat and SSR Analysis
3.3. IR Contraction and Expansion
3.4. Sequence Divergence and Divergence Hotspot
3.5. Phylogenomic Analysis
4. Discussion
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Sample Availability: Sequence data of two Lancea species are available from the authors. |
Characteristics | L. tibetica | L. hirsuta |
---|---|---|
Total cpDNA size (bp) | 153,664 | 154,045 |
Length of large single copy (LSC) region | 84,401 | 84,254 |
Length of inverted repeat (IR) region | 25,624 | 25,838 |
Length of small single copy (SSC) region | 18,016 | 17,781 |
Total GC content (%) | 37.9 | 37.9 |
LSC | 35.9 | 35.8 |
IR | 43.3 | 43.2 |
SSC | 30.0 | 32.0 |
Total number of genes | 106 | 105 |
Protein-coding genes | 79 | 79 |
rRNAs genes | 4 | 4 |
tRNAs genes | 23 | 22 |
Category | Name |
---|---|
Rubisco | rbcL |
Photosystem I | psaA, B, C, I, J |
Photosystem II | psbA, B, C, D, E, F, H, I, J, K, L, M, N, T, Z |
ATP synthase | atpA, B, E, * F, H, I |
Cytochrome b/f complex | petA, * B, * D, G, L, N |
Cytochrome c synthesis | ccsA |
NADPH dehydrogenase | * ndhA, *,a B, C, D, E, F, G, H, I, J, K |
Transcription | rpoA, B, * C1, C2 |
Small subunit ribosomal proteins | rps2, 3, 4, a 7, 8, 11, ** 12, 14, 15, * 16, 18, 19, |
Large subunit ribosomal proteins | *,a rpl2, 14, * 16, 20, 22, a 23, 32 33, 36 |
Translation initiation factor | infA |
Ribosomal RNA | a rrn4.5, a 5, a 16, a 23 |
RNA processing | matK |
Carbon metabolism | cemA |
Fatty acid synthesis | accD |
Proteolysis | ** c1pP |
Unknown function protein-coding gene | ycf1, 2, ** 3, 4 |
Transfer RNA | trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCC, trnH-GUG, a trnI-CAU, a trnL-CAA, trnL-UAG, a trnM-CAU, a trnN-GUU, trnP-UGG, trnQ-UUG, a trnR-ACG, trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, b trnT-UGU, a trnV-GAC, trnW-CCA, trnY-GUA |
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Chi, X.; Wang, J.; Gao, Q.; Zhang, F.; Chen, S. The Complete Chloroplast Genomes of Two Lancea Species with Comparative Analysis. Molecules 2018, 23, 602. https://doi.org/10.3390/molecules23030602
Chi X, Wang J, Gao Q, Zhang F, Chen S. The Complete Chloroplast Genomes of Two Lancea Species with Comparative Analysis. Molecules. 2018; 23(3):602. https://doi.org/10.3390/molecules23030602
Chicago/Turabian StyleChi, Xiaofeng, Jiuli Wang, Qingbo Gao, Faqi Zhang, and Shilong Chen. 2018. "The Complete Chloroplast Genomes of Two Lancea Species with Comparative Analysis" Molecules 23, no. 3: 602. https://doi.org/10.3390/molecules23030602