Codon Usage Bias Analysis of Citrus tristeza virus: Higher Codon Adaptation to Citrus reticulata Host
Abstract
:1. Introduction
2. Materials and Methods
2.1. Dataset
2.2. Nucleotide Composition Analysis and Effective Number of Codons (ENc)
2.3. ENc-GC3 Plot and Neutrality Plot
2.4. Relative Synonymous Codon Usage (RSCU) and Contribution of High-Frequency Codon (CHFC)
2.5. Codon Adaptation Index (CAI)
2.6. Correspondence Analysis (COA)
2.7. Statistical Analysis
3. Results and Discussion
3.1. Preference of G/U-Ended Codon Over A/C-Ended Codon in the AU-Rich CTV CP Gene
3.2. CTVCP Gene Displays Low Codon Usage Bias (CUB) and Higher Genomic Stability
3.3. Natural Selection and Mutation Pressure Both Play Roles in Codon Usage Bias of CTV
3.4. Natural Selection Plays Key Role in Shaping the Codon Usage Bias of CTV
3.5. Codon Usage Bias Has Significant Correlation with the Nucleotide Compositional Constraint in CTV
3.6. Higher Codon Usage Variation in Ca-CTV Subgroup
3.7. G/U-Ended Codons Display Higher Influence on Codon Usage of CTV
3.8. The High-Frequency Codons Are Evolutionarily Conserved in CTV
3.9. The Codon Usage Pattern of Cs-CTV Is Different from That of Ca-and Cr-CTV
3.10. CTV CP Gene Exhibits Higher Codon Usage Bias toward U-Ending Codons
3.11. CTV Is Biased toward Its Host Codon Usage Pattern
3.12. CTV Shows Mixture of Coincident and Antagonistic Codon Usage Patterns to Its Respective Host
3.13. Host-Preferred High-Frequency Codons Exert Greater Effect on the Codon Usage of CTV
3.14. Varied Degrees of CTV Codon Usage Adaptation to Different Citrus Hosts
3.15. Cr-CTV Isolates Display Higher Codon Usage Adaptation to C. reticulata Host
3.16. The Correlation between Varied Magnitude of High-Frequency Codons and Host–Virus Interactions
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Nt Composition | Ca-CTV | Cr-CTV | Cs-CTV | Overall CTV |
---|---|---|---|---|
A% | 28.78 (0.10) | 28.72 (0.26) | 28.71 (0.48) | 28.73 (0.05) |
C% | 18.41 (0.36) | 18.30 (0.51) | 18.42 (0.66) | 18.38 (0.04) |
U% | 26.91 (0.09) | 27.06 (0.29) | 26.98 (0.51) | 26.99 (0.03) |
G% | 25.90 (0.15) | 25.92 (0.33) | 25.88 (0.53) | 25.90 (0.05) |
GC% | 44.31 (0.53) | 44.23 (0.18) | 44.30 (0.20) | 44.28 (0.05) |
AU% | 55.69 (0.91) | 55.77 (0.47) | 55.70 (0.07) | 55.72 (0.05) |
A3% | 21.09 (0.40) | 20.64 (0.53) | 20.69 (0.65) | 20.77 (0.14) |
C3% | 20.26 (0.33) | 19.92 (0.49) | 20.40 (0.64) | 20.22 (0.09) |
U3% | 33.84 (0.24) | 34.26 (0.17) | 33.86 (0.40) | 33.98 (0.09) |
G3% | 24.82 (0.34) | 25.18 (0.43) | 25.06 (0.59) | 25.04 (0.15) |
GC3% | 45.07 (0.61) | 45.10 (0.32) | 45.45 (0.25) | 45.25 (0.13) |
GA3% | 45.91 (0.58) | 45.82 (0.23) | 45.75 (0.19) | 45.81 (0.06) |
GU3% | 58.65 (1.08) | 59.43 (0.65) | 58.91(0.32) | 59.01 (0.20) |
AU3% | 54.93 (0.92) | 54.90 (0.51) | 54.55(0.19) | 54.75 (0.13) |
CU3% | 54.09 (0.86) | 54.18 (0.44) | 54.25 (0.08) | 54.19 (0.06) |
GC1 | 0.50 (0.00) | 0.50 (0.00) | 0.50 (0.00) | 0.50 (0.00) |
GC2 | 0.38 (0.00) | 0.38 (0.00) | 0.38 (0.00) | 0.38 (0.00) |
GC3 | 0.44 (0.00) | 0.44 (0.00) | 0.44 (0.00) | 0.44 (0.00) |
GC12 | 0.44 (0.00) | 0.44 (0.01) | 0.44 (0.01) | 0.44(0.01) |
CBI | 0.05 (0.01) | 0.04 (0.00) | 0.04 (0.00) | 0.05 (0.00) |
Fop | 0.45 (0.00) | 0.45 (0.00) | 0.45 (0.00) | 0.45 (0.00) |
ENc | 54.63 (0.46) | 53.51 (0.39) | 53.74 (0.30) | 53.88 (0.22) |
L_sym | 216.69 (0.08) | 216.76 (0.08) | 216.78 (0.07) | 216.75 (0.04) |
L_aa | 223.00 (0.00) | 223.00 (0.00) | 223.00 (0.00) | 223.00 (0.00) |
Gravy | −0.48 (0.00) | −0.49 (0.00) | −0.48 (0.00) | −0.48 (0.00) |
Aromo | 0.08 (0.00) | 0.08 (0.00) | 0.08 (0.00) | 0.08 (0.00) |
CAI | CBI | Fop | ENc | GC1 | GC2 | GC12 | GC3 | A | C | U | G | GU | AC | GU3 | AU3 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CAI | ||||||||||||||||
CBI | 0.820 ** | |||||||||||||||
Fop | 0.826 ** | 0.998 ** | ||||||||||||||
ENc | 0.487 ** | 0.454 ** | 0.435 ** | |||||||||||||
GC1 | 0.387 ** | 0.247 ** | 0.233 ** | 0.610 ** | ||||||||||||
GC2 | −0.278 ** | −0.178 * | −0.172 | 0.047 | 0.056 | |||||||||||
GC12 | 0.151 | 0.096 | 0.088 | 0.512 ** | 0.827 ** | 0.608 ** | ||||||||||
GC3 | −0.563 ** | −0.412 ** | −0.402 ** | −0.373 ** | −0.329 ** | 0.093 | −0.210 * | |||||||||
A | 0.733 ** | 0.704 ** | 0.696 ** | 0.500 ** | 0.191 * | −0.268 ** | 0.001 | −0.795 ** | ||||||||
C | 0.425 ** | 0.665 ** | 0.653 ** | 0.614 ** | 0.382 ** | 0.090 | 0.355 ** | 0.005 | 0.388 ** | −0.845 ** | ||||||
U | −0.393 ** | −0.506 ** | −0.504 ** | −0.595 ** | −0.426 ** | −0.175 | −0.438 ** | −0.087 | −0.358 ** | −0.537 ** | 0.313 ** | |||||
G | −0.704 ** | −0.778 ** | −0.764 ** | −0.514 ** | −0.182 * | 0.273 ** | 0.009 | 0.741 ** | −0.931 ** | −0.788 ** | 0.686 ** | 0.906 ** | ||||
GU | −0.715 ** | −0.822 ** | −0.810 ** | −0.659 ** | −0.329 ** | 0.131 | −0.188 * | 0.529 ** | −0.874 ** | 0.788 ** | −0.686 ** | −0.906 ** | −0.471 ** | |||
AC | 0.715 ** | 0.822 ** | 0.810 ** | 0.659 ** | 0.329 ** | −0.131 | 0.188 * | −0.529 ** | 0.874 ** | −0.725 ** | 0.605 ** | 0.873 ** | 0.938 ** | −0.938 ** | ||
GU3 | −0.749 ** | −0.836 ** | −0.821 ** | −0.646 ** | −0.282 ** | 0.118 | −0.158 | 0.521 ** | −0.831 ** | 0.000 | 0.097 | −0.748 ** | −0.530 ** | 0.530 ** | −1.000 ** | |
AU3 | 0.568 ** | 0.431 ** | 0.420 ** | 0.370 ** | 0.325 ** | −0.090 | 0.208 * | −0.996 ** | 0.793 ** | 0.000 | −0.097 | 0.748 ** | 0.530 ** | −0.530 ** | 0.526 ** | −1.000 ** |
AA | Codon | Ca-CTV | Cr-CTV | Cs-CTV | C. aurantifolia (Ca) | C. reticulata (Cr) | C. sinensis (Cs) |
---|---|---|---|---|---|---|---|
Phe | UUU | 1.11 | 1.14 | 1.01 | 1.20 | 1.08 | 1.24 |
UUC | 0.89 | 0.86 | 0.99 | 0.80 | 0.92 | 0.76 | |
Leu | UUA | 1.54 | 1.40 | 1.47 | 0.95 | 0.88 | 0.87 |
UUG | 2.54 | 2.70 | 2.62 | 1.49 | 1.52 | 1.56 | |
CUU | 1.13 | 1.12 | 1.13 | 1.40 | 1.28 | 1.48 | |
CUC | 0.01 | 0.01 | 0.01 | 1.16 | 0.91 | 0.71 | |
CUA | 0.24 | 0.26 | 0.31 | 0.48 | 0.43 | 0.57 | |
CUG | 0.54 | 0.50 | 0.46 | 0.52 | 0.98 | 0.82 | |
Ile | AUU | 0.91 | 0.81 | 0.80 | 1.39 | 1.48 | 1.51 |
AUC | 0.50 | 0.59 | 0.55 | 0.93 | 0.90 | 0.71 | |
AUA | 1.59 | 1.6 | 1.65 | 0.68 | 0.63 | 0.77 | |
Val | GUU | 1.34 | 1.37 | 1.35 | 1.57 | 1.34 | 1.65 |
GUC | 1.00 | 1.01 | 1.07 | 0.90 | 0.84 | 0.63 | |
GUA | 0.51 | 0.48 | 0.37 | 0.55 | 0.54 | 0.66 | |
GUG | 1.15 | 1.13 | 1.21 | 0.98 | 1.29 | 1.06 | |
Pro | CCU | 1.49 | 1.44 | 1.38 | 1.84 | 1.54 | 1.50 |
CCC | 0.03 | 0.04 | 0.06 | 0.66 | 0.69 | 0.58 | |
CCA | 0.37 | 0.22 | 0.28 | 1.18 | 1.29 | 1.46 | |
CCG | 2.11 | 2.30 | 2.28 | 0.32 | 0.49 | 0.45 | |
Thr | ACU | 1.72 | 1.86 | 1.84 | 1.20 | 1.49 | 1.48 |
ACC | 0.89 | 0.78 | 0.77 | 0.99 | 0.84 | 0.75 | |
ACA | 0.66 | 0.64 | 0.65 | 1.34 | 1.21 | 1.36 | |
ACG | 0.73 | 0.72 | 0.73 | 0.47 | 0.45 | 0.42 | |
Ala | GCU | 1.90 | 1.86 | 1.85 | 1.88 | 1.41 | 1.65 |
GCC | 0.76 | 0.82 | 0.87 | 1.08 | 1.01 | 0.69 | |
GCA | 0.88 | 0.84 | 0.83 | 0.78 | 1.13 | 1.34 | |
GCG | 0.47 | 0.48 | 0.44 | 0.25 | 0.46 | 0.32 | |
Tyr | UAU | 1.29 | 1.28 | 1.29 | 0.94 | 1.03 | 1.23 |
UAC | 0.71 | 0.72 | 0.71 | 1.06 | 0.97 | 0.77 | |
Ser | UCU | 2.27 | 2.42 | 2.42 | 1.68 | 1.41 | 1.56 |
UCC | 0.71 | 0.56 | 0.53 | 0.96 | 0.84 | 0.72 | |
UCA | 0.75 | 0.84 | 0.81 | 1.20 | 1.33 | 1.45 | |
UCG | 0.38 | 0.32 | 0.30 | 0.48 | 0.69 | 0.42 | |
AGU | 1.45 | 1.57 | 1.53 | 0.80 | 0.87 | 1.07 | |
AGC | 0.44 | 0.29 | 0.41 | 0.89 | 0.85 | 0.77 | |
Arg | AGA | 1.18 | 1.09 | 1.12 | 2.38 | 1.84 | 1.98 |
AGG | 0.69 | 0.75 | 0.76 | 0.83 | 1.29 | 1.49 | |
CGU | 2.18 | 2.21 | 2.21 | 0.89 | 0.91 | 0.79 | |
CGC | 0.55 | 0.49 | 0.53 | 0.49 | 0.70 | 0.48 | |
CGA | 0.95 | 1.01 | 0.92 | 0.89 | 0.69 | 0.70 | |
CGG | 0.45 | 0.44 | 0.47 | 0.52 | 0.56 | 0.55 | |
Cys | UGU | 2.00 | 1.95 | 1.95 | 0.97 | 0.76 | 1.13 |
UGC | 0.00 | 0.05 | 0.05 | 1.03 | 1.24 | 0.87 | |
His | CAU | 0.59 | 0.62 | 0.61 | 1.15 | 1.05 | 1.32 |
CAC | 1.41 | 1.38 | 1.39 | 0.85 | 0.95 | 0.68 | |
Gln | CAA | 1.01 | 1.04 | 1.02 | 1.02 | 1.00 | 1.10 |
CAG | 0.99 | 0.96 | 0.98 | 0.98 | 1.00 | 0.90 | |
Asn | AAU | 0.52 | 0.59 | 0.59 | 0.83 | 1.11 | 1.30 |
AAC | 1.48 | 1.41 | 1.41 | 1.17 | 0.89 | 0.70 | |
Lys | AAA | 0.84 | 0.84 | 0.79 | 1.05 | 0.93 | 0.99 |
AAG | 1.16 | 1.16 | 1.21 | 0.95 | 1.07 | 1.01 | |
Asp | GAU | 1.16 | 1.17 | 1.16 | 1.29 | 1.33 | 1.42 |
GAC | 0.84 | 0.83 | 0.84 | 0.71 | 0.67 | 0.58 | |
Glu | GAA | 1.32 | 1.26 | 1.35 | 1.04 | 0.99 | 1.10 |
GAG | 0.68 | 0.74 | 0.65 | 0.96 | 1.01 | 0.90 | |
Gly | GGU | 1.62 | 1.54 | 1.48 | 1.26 | 1.09 | 1.20 |
GGC | 0.65 | 0.73 | 0.75 | 1.11 | 0.98 | 0.73 | |
GGA | 0.76 | 0.74 | 0.77 | 1.13 | 1.21 | 1.29 | |
GGG | 0.97 | 1.00 | 0.99 | 0.50 | 0.71 | 0.77 | |
Trp | UGG | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
Met | AUG | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 |
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Biswas, K.K.; Palchoudhury, S.; Chakraborty, P.; Bhattacharyya, U.K.; Ghosh, D.K.; Debnath, P.; Ramadugu, C.; Keremane, M.L.; Khetarpal, R.K.; Lee, R.F. Codon Usage Bias Analysis of Citrus tristeza virus: Higher Codon Adaptation to Citrus reticulata Host. Viruses 2019, 11, 331. https://doi.org/10.3390/v11040331
Biswas KK, Palchoudhury S, Chakraborty P, Bhattacharyya UK, Ghosh DK, Debnath P, Ramadugu C, Keremane ML, Khetarpal RK, Lee RF. Codon Usage Bias Analysis of Citrus tristeza virus: Higher Codon Adaptation to Citrus reticulata Host. Viruses. 2019; 11(4):331. https://doi.org/10.3390/v11040331
Chicago/Turabian StyleBiswas, Kajal Kumar, Supratik Palchoudhury, Prosenjit Chakraborty, Utpal K. Bhattacharyya, Dilip K. Ghosh, Palash Debnath, Chandrika Ramadugu, Manjunath L. Keremane, Ravi K. Khetarpal, and Richard F. Lee. 2019. "Codon Usage Bias Analysis of Citrus tristeza virus: Higher Codon Adaptation to Citrus reticulata Host" Viruses 11, no. 4: 331. https://doi.org/10.3390/v11040331