The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis
Abstract
:1. Introduction
2. Results and Discussion
2.1. Gene Content and Structure of Chloroplast Genome of Oreocharis esquirolii
2.2. Codon Usage Bias Analysis
2.3. SSRs Analysis
2.4. Analysis of Repeat Sequences
2.5. Comparisons of Chloroplast Genome among Oreocharis esquirolii and Closely Related Species
2.6. Phylogenetic Position of Oreocharis esquirolii
3. Materials and Methods
3.1. Plant Material, DNA Extraction, Sequencing, and Assembly
3.2. Genome Annotation and Sequence Submission
3.3. Codon Usage, Repetitive Sequence, and SSR Analysis
3.4. Genome Comparison
3.5. Phylogenetic Analyses
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Category | Gene Group | Gene Names |
---|---|---|
Photosynthesis | Subunits of ATP synthase | atpA, atpB, atpE, atpF *, atpI, atpH |
Subunits of NADH dehydrogenase | ndhA *, ndhB * (×2), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK, | |
Subunits of cytochrome | petA, petB, petD, petG, petL, petN | |
Subunits of photosystem I | psaA, psaB, psaC, psaJ, psaI | |
Subunits of photosystem II | psbA, psbB, psbC, psbD, psbE, psbH, psbK, psbN, psbJ, psbF, psbL, psbI, psbM, psbT, psbZ | |
Subunit of rubisco | rbcL | |
Other genes | Subunit of Acetyl-CoA-carboxylase | accD |
c-type cytochrome synthesis gene | ccsA | |
Envelop membrane protein | cemA | |
Protease | clpP ** | |
Translational initiation | infA | |
Maturase | matK | |
Self-replication | Large subunit of ribosome | rpl2 * (×2), rpl14, rpl16 *, rpl20, rpl22, rpl23 (×2), rpl32, rpl33, rpl36 |
DNA dependent RNA polymerase | rpoA, rpoC2, rpoB, rpoC1 | |
Small subunit of ribosome | rps12 ** (×2), rps2, rps3, rps4, rps7 (×2), rps8, rps11, rps14, rps15, rps16 *, rps18, rps19 | |
rRNA Genes | rrn4.5 (×2), rrn5 (×2), rrn16 (×2), rrn23 (×2) | |
tRNA Genes | trnK-UUU *, trnI-GAU * (×2), trnA-UGC * (×2), trnV-UAC *, trnL-UAA *, trnS-UGA, trnS-GCU, trnS-GGA, trnY-GUA, trnL-CAA (×2), trnL-UAG, trnL-GAG, trnM-CAU, trnR-ACG (×2), trnP-UGG, trnW-CCA, trnD-GUC, trnH-GUG, trnF-GAA, trnT-UGU, trnE-UUC, trnN-GUU (×2), trnV-GAC (×2), trnT-GGU, trnQ-UUG, trnR-UCU, trnG-GCC, trnC-GCA, trnI-CAU (×2), trnfM-CAU | |
Unknown function | Conserved open reading frames | ycf1 (×2, ψ), ycf2 (×2), ycf3 **, ycf4, ycf15 (×2) |
Gene | Region | Exon1 (bp) | Intron1 (bp) | Exon2 (bp) | Intron2 (bp) | Exon3 (bp) |
---|---|---|---|---|---|---|
atpF | LSC | 144 | 707 | 411 | ||
ndhA | SSC | 552 | 1062 | 540 | ||
ndhB | IR | 777 | 679 | 756 | ||
rpl2 | IR | 390 | 673 | 435 | ||
rpl16 | LSC | 9 | 824 | 399 | ||
rps16 | LSC | 42 | 921 | 210 | ||
clpP | LSC | 69 | 814 | 291 | 644 | 228 |
rpoC1 | LSC | 453 | 812 | 1611 | ||
trnA-UGC | IR | 38 | 807 | 35 | ||
trnI-GAU | IR | 37 | 941 | 35 | ||
trnK-UUU | LSC | 37 | 2497 | 36 | ||
trnL-UAA | LSC | 37 | 476 | 48 | ||
trnV-UAC | LSC | 38 | 586 | 35 | ||
ycf3 | LSC | 126 | 692 | 228 | 714 | 153 |
Region | Length (bp) | A (%) | T (%) | G (%) | C (%) | GC (%) |
---|---|---|---|---|---|---|
LSC | 85,156 | 31.54 | 33.03 | 17.30 | 18.13 | 35.43 |
SSC | 18,129 | 34.34 | 34.50 | 15.00 | 16.16 | 31.16 |
IRA | 25,392 | 28.38 | 28.41 | 22.42 | 20.79 | 43.21 |
IRB | 25,392 | 28.38 | 28.41 | 22.42 | 20.79 | 43.21 |
CDS | 79,650 | 30.70 | 31.59 | 20.10 | 17.61 | 37.71 |
Total genome | 154,069 | 30.83 | 31.67 | 18.45 | 19.04 | 37.49 |
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Gu, L.; Su, T.; An, M.-T.; Hu, G.-X. The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis. Plants 2020, 9, 1692. https://doi.org/10.3390/plants9121692
Gu L, Su T, An M-T, Hu G-X. The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis. Plants. 2020; 9(12):1692. https://doi.org/10.3390/plants9121692
Chicago/Turabian StyleGu, Li, Ting Su, Ming-Tai An, and Guo-Xiong Hu. 2020. "The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis" Plants 9, no. 12: 1692. https://doi.org/10.3390/plants9121692