Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data Collection
2.2. Recombination Detection and Phylogenetic Analysis
2.3. Nucleotide Composition
2.4. Dinucleotide Relative Abundance Analysis
2.5. Codon Vias Analysis
2.5.1. Effective Number of Codons Analysis
2.5.2. Relative Synonymous Codon Usage Analysis
2.5.3. Principal Component Analysis
2.6. Codon Pair Bias Analysis
2.7. Codon Usage Comparison Between Viruses and Hosts
2.7.1. Codon Adaptation Index Analysis
2.7.2. Relative Codon Deoptimization Index Analysis
2.7.3. Similarity Index Analysis
2.8. Statistical Analysis
3. Results
3.1. Recombination and Phylogenetic Analysis
3.2. Nucleotide Composition
3.3. Dinucleotide Relative Abundance Analysis
3.4. Codon Bias and Codon Pair Bias Analysis
3.5. Codon Usage Comparison Between Virus and Host
3.6. JXA1-Attenuated Strain Analysis
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Categories | Lineage 1 | Lineage 3 | Lineage 5 | Lineage 8 | All |
---|---|---|---|---|---|
%A | 0.214 ± 0.004 | 0.210 ± 0.006 | 0.203 ± 0.002 | 0.201 ± 0.003 | 0.204 ± 0.006 |
%C | 0.236 ± 0.006 | 0.241 ± 0.007 | 0.244 ± 0.003 | 0.241 ± 0.003 | 0.240 ± 0.005 |
%U | 0.296 ± 0.006 | 0.295 ± 0.010 | 0.294 ± 0.003 | 0.295 ± 0.003 | 0.296 ± 0.005 |
%G | 0.254 ± 0.005 | 0.254 ± 0.007 | 0.259 ± 0.002 | 0.263 ± 0.003 | 0.260 ± 0.005 |
%A3 | 0.131 ± 0.008 | 0.135 ± 0.012 | 0.129 ± 0.004 | 0.118 ± 0.008 | 0.122 ± 0.011 |
%C3 | 0.318 ± 0.014 | 0.333 ± 0.021 | 0.324 ± 0.007 | 0.317 ± 0.006 | 0.320 ± 0.012 |
%U3 | 0.293 ± 0.014 | 0.283 ± 0.027 | 0.297 ± 0.005 | 0.290 ± 0.006 | 0.290 ± 0.012 |
%G3 | 0.258 ± 0.009 | 0.249 ± 0.015 | 0.250 ± 0.004 | 0.275 ± 0.008 | 0.268 ± 0.014 |
A3s | 0.183 ± 0.011 | 0.186 ± 0.016 | 0.178 ± 0.005 | 0.163 ± 0.011 | 0.169 ± 0.015 |
C3s | 0.365 ± 0.016 | 0.382 ± 0.025 | 0.372 ± 0.007 | 0.361 ± 0.007 | 0.365 ± 0.014 |
U3s | 0.336 ± 0.015 | 0.324 ± 0.030 | 0.341 ± 0.007 | 0.330 ± 0.007 | 0.331 ± 0.014 |
G3s | 0.323 ± 0.015 | 0.309 ± 0.020 | 0.303 ± 0.007 | 0.341 ± 0.013 | 0.333 ± 0.019 |
%G + C | 0.490 ± 0.007 | 0.495 ± 0.011 | 0.502 ± 0.004 | 0.504 ± 0.004 | 0.501 ± 0.007 |
GC1s | 0.452 ± 0.007 | 0.451 ± 0.010 | 0.481 ± 0.004 | 0.475 ± 0.006 | 0.469 ± 0.012 |
GC2s | 0.442 ± 0.009 | 0.451 ± 0.011 | 0.451 ± 0.004 | 0.444 ± 0.008 | 0.445 ± 0.009 |
GC3s | 0.576 ± 0.015 | 0.583 ± 0.031 | 0.574 ± 0.009 | 0.592 ± 0.010 | 0.588 ± 0.016 |
GC12s | 0.447 ± 0.006 | 0.451 ± 0.007 | 0.466 ± 0.003 | 0.459 ± 0.005 | 0.457 ± 0.007 |
ENC | 59.653 ± 1.643 | 59.618 ± 2.002 | 60.797 ± 0.624 | 59.645 ± 1.239 | 59.693 ± 1.406 |
Categories | Lineage 1 | Lineage 3 | Lineage 5 | Lineage 8 | All |
---|---|---|---|---|---|
UpU | 1.073 ± 0.048 | 1.128 ± 0.086 | 1.053 ± 0.029 | 1.075 ± 0.032 | 1.079 ± 0.047 |
UpC | 0.862 ± 0.045 | 0.965 ± 0.088 | 0.962 ± 0.023 | 0.911 ± 0.032 | 0.912 ± 0.052 |
UpA | 0.783 ± 0.060 | 0.716 ± 0.089 | 0.723 ± 0.020 | 0.710 ± 0.032 | 0.722 ± 0.053 |
UpG | 1.301 ± 0.052 | 1.235 ± 0.061 | 1.281 ± 0.014 | 1.315 ± 0.027 | 1.302 ± 0.044 |
CpU | 0.983 ± 0.048 | 1.000 ± 0.064 | 1.108 ± 0.036 | 1.156 ± 0.030 | 1.111 ± 0.082 |
CpC | 0.897 ± 0.050 | 0.822 ± 0.081 | 0.783 ± 0.025 | 0.712 ± 0.033 | 0.755 ± 0.082 |
CpA | 1.260 ± 0.074 | 1.284 ± 0.118 | 1.255 ± 0.028 | 1.344 ± 0.040 | 1.321 ± 0.069 |
CpG | 0.843 ± 0.065 | 0.850 ± 0.084 | 0.847 ± 0.029 | 0.749 ± 0.030 | 0.779 ± 0.064 |
ApU | 1.064 ± 0.065 | 0.979 ± 0.086 | 0.847 ± 0.039 | 0.913 ± 0.030 | 0.940 ± 0.074 |
ApC | 0.979 ± 0.063 | 0.951 ± 0.106 | 1.004 ± 0.026 | 1.113 ± 0.035 | 1.070 ± 0.083 |
ApA | 1.126 ± 0.087 | 1.106 ± 0.089 | 1.120 ± 0.019 | 0.944 ± 0.051 | 0.997 ± 0.101 |
ApG | 0.765 ± 0.055 | 0.903 ± 0.080 | 0.966 ± 0.043 | 0.968 ± 0.046 | 0.931 ± 0.088 |
GpU | 0.953 ± 0.047 | 0.984 ± 0.058 | 1.044 ± 0.023 | 0.935 ± 0.024 | 0.948 ± 0.042 |
GpC | 1.221 ± 0.053 | 1.163 ± 0.067 | 1.215 ± 0.024 | 1.201 ± 0.033 | 1.200 ± 0.044 |
GpA | 0.805 ± 0.057 | 0.868 ± 0.064 | 0.842 ± 0.026 | 0.958 ± 0.032 | 0.920 ± 0.072 |
GpG | 1.034 ± 0.057 | 0.978 ± 0.047 | 0.892 ± 0.019 | 0.930 ± 0.033 | 0.949 ± 0.055 |
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Wu, W.; Ge, X.; Zhang, Y.; Han, J.; Guo, X.; Zhou, L.; Yang, H. Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China. Viruses 2021, 13, 1044. https://doi.org/10.3390/v13061044
Wu W, Ge X, Zhang Y, Han J, Guo X, Zhou L, Yang H. Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China. Viruses. 2021; 13(6):1044. https://doi.org/10.3390/v13061044
Chicago/Turabian StyleWu, Weixin, Xinna Ge, Yongning Zhang, Jun Han, Xin Guo, Lei Zhou, and Hanchun Yang. 2021. "Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China" Viruses 13, no. 6: 1044. https://doi.org/10.3390/v13061044
APA StyleWu, W., Ge, X., Zhang, Y., Han, J., Guo, X., Zhou, L., & Yang, H. (2021). Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China. Viruses, 13(6), 1044. https://doi.org/10.3390/v13061044