The Complete Chloroplast Genome of An Ophiorrhiza baviensis Drake Species Reveals Its Molecular Structure, Comparative, and Phylogenetic Relationships
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Chloroplast Genome Sequencing
2.2. DNA Extraction and Chloroplast Genome Sequencing
2.3. Genome Assembly and Annotation
2.4. Genome Comparison and Phylogenetic Identification
3. Results
3.1. Chloroplast Genome Assembly and Annotation
3.2. Repeat Sequences and Codon Analysis
3.3. Chloroplast Genome Comparison
3.4. IR Contraction and Expansion in the Chloroplast Genome
3.5. Phylogenetic Inference
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Genome Features | O. baviensis Drake |
---|---|
Genome size (bp) | 154,770 bp |
LSC size (bp) | 84,826 |
SSC size (bp) | 18,574 |
IR size (bp) | 25,685 |
GC content (%) | 37.6 |
No. of genes | 128 |
No. of PCGs | 87 |
No. of tRNA | 33 |
No. of rRNA | 8 |
Category of Genes | Group of Genes | Name of Genes |
---|---|---|
Photosynthesis | Subunits of ATP synthase | atpA, atpB, atpE, atpFa, atpH, atpI |
Subunits of NADH-dehydrogenase | ndhAa, ndhB (×2)a, ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK | |
Subunits of cytochrome b/f complex | petL, petB, petG, petA, petD, petN | |
Subunits of photosystem I | psaJ, psaC, psaA, psaI, psaB | |
Subunits of photosystem II | psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ | |
Subunit of rubisco | rbcL | |
Transcription and translation | Large subunit of ribosome | rpl14, rpl16a, rpl2 (×2)a, rpl20, rpl22, rpl23 (×2), rpl32, rpl33, rpl36 |
DNA-dependent RNA polymerase | rpoB, rpoA, rpoC1a, rpoC2 | |
Small subunit of ribosomal proteins | rps11, rps12(×2)a, rps14, rps15, rps16a, rps18, rps19 (×2), rps2, rps3, rps4, rps7 (×2), rps8 | |
rRNA genes | rrn23S (×2), rrn16S (×2), rrn5S (×2), rrn4.5S (×2) | |
tRNA genes | trnA-UGC (×2)a, trnC-GCA, trnD-GUC, trnE-UUC, trnF-GAA, trnG-GCCa, trnH-GUG, trnI-GAU (×2)a, trnL-CAA (×2), trnL-UAG, trnN-GUU (×2), trnP-UGG, trnQ-UUG, trnR-ACG (×2), trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC (×2), trnW-CCA, trnY-GUA | |
Translational initiation factor | infA | |
Other genes | Subunit of acetyl-CoA-carboxylase (fatty acid synthesis) | accD |
c-type cytochrome synthesis gene | ccsA | |
Envelope membrane protein (carbon metabolism) | cemA | |
Protease | clpPb | |
Maturase (RNA processing) | matK | |
Conserved open reading frames | ycf1, ycf2 (×2), ycf3b |
Codon | AA | Frequency | RCSU | Codon | AA | Frequency | RCSU | Codon | AA | Frequency | RCSU |
---|---|---|---|---|---|---|---|---|---|---|---|
UAA | * | 1259 | 1.22 | AUC | I | 1205 | 0.80 | CGG | R | 420 | 0.75 |
UAG | * | 825 | 0.80 | AUA | I | 1471 | 0.98 | AGA | R | 1093 | 1.94 |
UGA | * | 1004 | 0.98 | AAA | K | 2050 | 1.35 | AGG | R | 627 | 1.12 |
GCU | A | 446 | 1.23 | AAG | K | 982 | 0.65 | UCU | S | 1113 | 1.39 |
GCC | A | 351 | 0.97 | UUA | L | 1040 | 1.23 | UCC | S | 982 | 1.22 |
GCA | A | 401 | 1.11 | UUG | L | 1095 | 1.30 | UCA | S | 824 | 1.03 |
GCG | A | 250 | 0.69 | CUU | L | 1063 | 1.26 | UCG | S | 622 | 0.77 |
UGU | C | 679 | 1.20 | CUC | L | 653 | 0.77 | AGU | S | 747 | 0.93 |
UGC | C | 449 | 0.80 | CUA | L | 737 | 0.87 | AGC | S | 529 | 0.66 |
GAU | D | 1012 | 1.42 | CUG | L | 480 | 0.57 | ACU | T | 668 | 1.13 |
GAC | D | 413 | 0.58 | AUG | M | 856 | 1.00 | ACC | T | 651 | 1.10 |
GAA | E | 1337 | 1.43 | AAU | N | 1779 | 1.38 | ACA | T | 647 | 1.09 |
GAG | E | 537 | 0.57 | AAC | N | 800 | 0.62 | ACG | T | 406 | 0.68 |
UUU | F | 2212 | 1.20 | CCU | P | 611 | 1.03 | GUU | V | 784 | 1.38 |
UUC | F | 1481 | 0.80 | CCC | P | 618 | 1.04 | GUC | V | 411 | 0.72 |
GGU | G | 540 | 0.96 | CCA | P | 726 | 1.23 | GUA | V | 682 | 1.20 |
GGC | G | 383 | 0.68 | CCG | P | 414 | 0.70 | GUG | V | 402 | 0.71 |
GGA | G | 747 | 1.33 | CAA | Q | 987 | 1.40 | UGG | W | 681 | 1.00 |
GGG | G | 577 | 1.03 | CAG | Q | 420 | 0.60 | UAU | Y | 1345 | 1.36 |
CAU | H | 880 | 1.36 | CGU | R | 376 | 0.67 | UAC | Y | 637 | 0.64 |
CAC | H | 414 | 0.64 | CGC | R | 280 | 0.50 | ||||
AUU | I | 1830 | 1.22 | CGA | R | 576 | 1.02 |
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Pham, M.H.; Tran, T.H.; Le, T.D.; Le, T.L.; Hoang, H.; Chu, H.H. The Complete Chloroplast Genome of An Ophiorrhiza baviensis Drake Species Reveals Its Molecular Structure, Comparative, and Phylogenetic Relationships. Genes 2023, 14, 227. https://doi.org/10.3390/genes14010227
Pham MH, Tran TH, Le TD, Le TL, Hoang H, Chu HH. The Complete Chloroplast Genome of An Ophiorrhiza baviensis Drake Species Reveals Its Molecular Structure, Comparative, and Phylogenetic Relationships. Genes. 2023; 14(1):227. https://doi.org/10.3390/genes14010227
Chicago/Turabian StylePham, Mai Huong, Thu Hoai Tran, Thi Dung Le, Tung Lam Le, Ha Hoang, and Hoang Ha Chu. 2023. "The Complete Chloroplast Genome of An Ophiorrhiza baviensis Drake Species Reveals Its Molecular Structure, Comparative, and Phylogenetic Relationships" Genes 14, no. 1: 227. https://doi.org/10.3390/genes14010227