Analysis of Codon Usage Bias in the Plastid Genome of Diplandrorchis sinica (Orchidaceae)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Acquisition of Sequence Data
2.2. Calculation of Codon-Related Parameters
2.3. Neutral Plot Analysis
2.4. ENC-Plot Analysis
2.5. PR2-Plot Analysis
2.6. Optimal Codon Analysis
2.7. Correspondence Analysis
2.8. Statistical Analysis
3. Results
3.1. Composition Characteristics of Codons
3.2. Neutral Plot Analysis
3.3. ENC-Plot Analysis
3.4. PR2-Plot Analysis
3.5. Optimal Codon Analysis
3.6. Correspondence Analysis
4. Discussion
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Genes | GC1 | GC2 | GC3 | GCall | GC12 | ENC | Laa |
---|---|---|---|---|---|---|---|
accD | 0.38 | 0.34 | 0.25 | 0.32 | 0.36 | 42 | 497 |
clpP | 0.59 | 0.37 | 0.31 | 0.42 | 0.48 | 56 | 195 |
ndhB | 0.38 | 0.35 | 0.31 | 0.35 | 0.36 | 44 | 237 |
ndhG | 0.32 | 0.29 | 0.30 | 0.30 | 0.30 | 51 | 135 |
psaB | 0.40 | 0.43 | 0.37 | 0.40 | 0.42 | 57 | 237 |
rbcL | 0.49 | 0.43 | 0.30 | 0.41 | 0.46 | 47 | 177 |
rpl14 | 0.51 | 0.37 | 0.24 | 0.37 | 0.44 | 47 | 122 |
rpl16 | 0.48 | 0.52 | 0.27 | 0.42 | 0.50 | 38 | 135 |
rpl20 | 0.37 | 0.37 | 0.27 | 0.34 | 0.37 | 53 | 133 |
rpl22 | 0.46 | 0.35 | 0.23 | 0.35 | 0.40 | 50 | 124 |
rps11 | 0.53 | 0.53 | 0.22 | 0.42 | 0.53 | 46 | 138 |
rps12 | 0.52 | 0.48 | 0.25 | 0.42 | 0.50 | 44 | 123 |
rps14 | 0.43 | 0.48 | 0.25 | 0.38 | 0.45 | 36 | 100 |
rps2 | 0.41 | 0.39 | 0.27 | 0.36 | 0.40 | 43 | 287 |
rps3 | 0.45 | 0.35 | 0.25 | 0.35 | 0.40 | 48 | 221 |
rps4 | 0.47 | 0.36 | 0.28 | 0.37 | 0.41 | 50 | 204 |
rps7 | 0.54 | 0.46 | 0.24 | 0.41 | 0.50 | 48 | 155 |
rps8 | 0.41 | 0.38 | 0.22 | 0.34 | 0.39 | 35 | 131 |
ycf1 | 0.36 | 0.27 | 0.27 | 0.30 | 0.32 | 48 | 1763 |
ycf2 | 0.42 | 0.35 | 0.37 | 0.38 | 0.38 | 51 | 2250 |
Average | 0.45 | 0.39 | 0.27 | 0.37 | 0.42 | 47 | 368 |
Amino Acid | Codon | High Expressed Gene | Low Expressed Gene | ΔRSCU | ||
---|---|---|---|---|---|---|
Number | RSCU | Number | RSCU | |||
S (Ser) | UCU ## | 115 | 1.76 | 29 | 1.45 | 0.31 |
UCC ### | 82 | 1.26 | 13 | 0.65 | 0.61 | |
UCA # | 84 | 1.29 | 23 | 1.15 | 0.14 | |
UCG # | 30 | 0.46 | 4 | 0.2 | 0.26 | |
AGU | 60 | 0.92 | 44 | 2.2 | −1.28 | |
AGC | 20 | 0.31 | 7 | 0.35 | −0.04 | |
P (Pro) | CCU | 59 | 1.48 | 21 | 1.91 | −0.43 |
CCC | 32 | 0.81 | 9 | 0.82 | −0.01 | |
CCA | 50 | 1.26 | 14 | 1.27 | −0.01 | |
CCG ## | 18 | 0.45 | 0 | 0 | 0.45 | |
A (Ala) | GCU | 42 | 1.5 | 28 | 2.15 | −0.65 |
GCC | 18 | 0.64 | 9 | 0.69 | −0.05 | |
GCA ### | 38 | 1.36 | 11 | 0.85 | 0.51 | |
GCG # | 14 | 0.5 | 4 | 0.31 | 0.19 | |
L (Leu) | UUA | 118 | 1.55 | 30 | 1.53 | 0.02 |
UUG # | 100 | 1.31 | 23 | 1.17 | 0.14 | |
CUU | 94 | 1.23 | 31 | 1.58 | −0.35 | |
CUC | 34 | 0.45 | 9 | 0.46 | −0.01 | |
CUA | 69 | 0.91 | 19 | 0.97 | −0.06 | |
CUG # | 42 | 0.55 | 6 | 0.31 | 0.24 | |
I (Ile) | AUU | 163 | 1.29 | 62 | 1.54 | −0.25 |
AUC | 76 | 0.6 | 29 | 0.72 | −0.12 | |
AUA ## | 141 | 1.11 | 30 | 0.74 | 0.37 | |
V (Val) | GUU | 67 | 1.61 | 27 | 1.54 | 0.07 |
GUC ## | 26 | 0.63 | 5 | 0.29 | 0.34 | |
GUA | 46 | 1.11 | 32 | 1.83 | −0.72 | |
GUG ## | 27 | 0.65 | 6 | 0.34 | 0.31 | |
N (Asn) | AAU | 216 | 1.51 | 45 | 1.61 | −0.10 |
AAC # | 71 | 0.49 | 11 | 0.39 | 0.10 | |
K (Lys) | AAA | 288 | 1.42 | 35 | 1.52 | −0.10 |
AAG # | 117 | 0.58 | 11 | 0.48 | 0.10 | |
Y (Tyr) | UAU | 125 | 1.54 | 41 | 1.55 | −0.01 |
UAC | 37 | 0.46 | 12 | 0.45 | 0.01 | |
H (His) | CAU | 82 | 1.53 | 20 | 1.74 | −0.21 |
CAC # | 25 | 0.47 | 3 | 0.26 | 0.21 | |
Q (Gln) | CAA | 141 | 1.54 | 29 | 1.49 | 0.05 |
CAG | 42 | 0.46 | 10 | 0.51 | −0.05 | |
T (Thr) | ACU | 67 | 1.39 | 22 | 1.49 | −0.10 |
ACC | 32 | 0.66 | 12 | 0.81 | −0.15 | |
ACA | 65 | 1.35 | 21 | 1.42 | −0.07 | |
ACG ## | 29 | 0.6 | 4 | 0.27 | 0.33 | |
C (Cys) | UGU | 39 | 1.34 | 16 | 1.6 | −0.26 |
UGC # | 19 | 0.66 | 4 | 0.4 | 0.26 | |
F (Phe) | UUU | 172 | 1.2 | 54 | 1.3 | −0.10 |
UUC # | 114 | 0.8 | 29 | 0.7 | 0.10 | |
R (Arg) | CGU # | 45 | 0.93 | 6 | 0.75 | 0.18 |
CGC | 18 | 0.37 | 4 | 0.5 | −0.13 | |
CGA ## | 64 | 1.32 | 8 | 1 | 0.32 | |
CGG | 26 | 0.54 | 4 | 0.5 | 0.04 | |
AGA | 107 | 2.21 | 18 | 2.25 | −0.04 | |
AGG | 30 | 0.62 | 8 | 1 | −0.38 | |
* (TER) | UGA # | 2 | 1.2 | 0 | 0 | 1.20 |
UAA | 2 | 1.2 | 4 | 2.4 | −1.20 | |
UAG | 1 | 0.6 | 1 | 0.6 | 0 | |
G (Gly) | GGU # | 43 | 0.99 | 15 | 0.88 | 0.11 |
GGC | 15 | 0.34 | 12 | 0.71 | −0.37 | |
GGA | 76 | 1.75 | 33 | 1.94 | −0.19 | |
GGG ## | 40 | 0.92 | 8 | 0.47 | 0.45 | |
D (Asp) | GAU | 193 | 1.65 | 45 | 1.7 | −0.05 |
GAC | 41 | 0.35 | 8 | 0.3 | 0.05 | |
E (Glu) | GAA | 203 | 1.41 | 49 | 1.48 | −0.07 |
GAG | 84 | 0.59 | 17 | 0.52 | 0.07 |
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Chen, X.; Zhao, Y.; Xu, S.; Zhou, Y.; Zhang, L.; Qu, B.; Xu, Y. Analysis of Codon Usage Bias in the Plastid Genome of Diplandrorchis sinica (Orchidaceae). Curr. Issues Mol. Biol. 2024, 46, 9807-9820. https://doi.org/10.3390/cimb46090582
Chen X, Zhao Y, Xu S, Zhou Y, Zhang L, Qu B, Xu Y. Analysis of Codon Usage Bias in the Plastid Genome of Diplandrorchis sinica (Orchidaceae). Current Issues in Molecular Biology. 2024; 46(9):9807-9820. https://doi.org/10.3390/cimb46090582
Chicago/Turabian StyleChen, Xuhui, Yudi Zhao, Shenghua Xu, Yingze Zhou, Lijie Zhang, Bo Qu, and Yufeng Xu. 2024. "Analysis of Codon Usage Bias in the Plastid Genome of Diplandrorchis sinica (Orchidaceae)" Current Issues in Molecular Biology 46, no. 9: 9807-9820. https://doi.org/10.3390/cimb46090582