Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae
Abstract
:1. Introduction
2. Results
2.1. Bias A/T versus G/C in Chlamydia spp. Genes
2.2. Nucleotide Usage Bias at Gene Levels of Chlamydia spp.
2.3. Nucleotide Usage Influencing Codon Usage
2.4. Genetic Diversity of Chlamydia spp. in Codon and Amino Acid Usage
2.5. Multiple Selection Forces Influencing Codon Usage Patterns in Chlamydia spp.
2.6. High Codon Usage Adaptation of T3ss and Pmps Gene Families to that of Corresponding Genome
3. Discussion
4. Materials and Methods
4.1. The Genome Data
4.2. Nucleotide Usage Patterns by Information Entropy
4.3. Relative Synonymous Codon Usage (RSCU) Value
4.4. Amino Acid Usage Bias by Information Entropy
4.5. Genetic Diversity of Chlamydia at Synonymous Codon and Amino Acid Usages
4.6. Codon Usage Index
4.7. Similarity of Codon Usage
4.8. Statistical Methods
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
ENC | Effective Number of Codons |
CAI | Codon Adaptation Index |
RSCU | Relative Synonymous Codon Usage |
PCA | Principal Component Analysis |
Pmps | Polymorphic membrane proteins |
T3ss | Type III secretion system |
References
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Species | T% | C% | A% | G% | T3% | C3% | A3% | G3% |
---|---|---|---|---|---|---|---|---|
C. trachomatis L2/25567R | 29.9 ± 3.18 | 20 ± 3.37 | 28.4 ± 3.31 | 21.7 ± 3.38 | 36.5 ± 4 | 16.6 ± 5.05 | 29.01 ± 3.93 | 17.9 ± 4.73 |
C. trachomatis A-Har-13 | 29.9 ± 3.39 | 20 ± 3.43 | 28.5 ± 3.49 | 21.6 ± 3.61 | 36 ± 4.27 | 16.6 ± 5.12 | 29.1 ± 4.15 | 17.9 ± 4.84 |
C. trachomatis ESW3 | 29.9 ± 3.2 | 20 ± 3.37 | 28.4 ± 3.34 | 21.7 ± 3.4 | 29.9 ± 3.2 | 20 ± 3.37 | 28.4 ± 3.34 | 21.7 ± 3.4 |
C. suis MD56 | 29.5 ± 3.5 | 20.4 ± 3.5 | 28.1 ± 3.7 | 22 ± 3.7 | 35 ± 4.4 | 17.5 ± 5.3 | 28.2 ± 4.3 | 19.0 ± 5.2 |
C. muridarum Nigg | 30.5 ± 3.3 | 19.5 ± 3.3 | 28.8 ± 3.5 | 21.2 ± 3.7 | 38 ± 4.1 | 15.6 ± 5.0 | 29.5 ± 4.2 | 17.3 ± 5.0 |
C. abortus S26/3 | 29.9 ± 3.4 | 19.8 ± 2.8 | 29.7 ± 3.5 | 20.6 ± 2.9 | 36 ± 4.5 | 17.3 ± 4.4 | 29.8 ± 4.3 | 16.8 ± 4.0 |
C. psittaci 6BC | 30.2 ± 3.3 | 19.4 ± 2.6 | 30.1 ± 3.4 | 20.3 ± 2.8 | 38 ± 4.3 | 16.2 ± 4.3 | 30.8 ± 4.3 | 15.5 ± 3.7 |
C. pecorum E58 | 29.5 ± 3.8 | 20.3 ± 4.0 | 28.8 ± 4.1 | 21.3 ± 3.9 | 36 ± 5.3 | 17.3 ± 6.1 | 28.4 ± 5.3 | 18.6 ± 5.5 |
C. pneumoniae TW-183 | 29.5 ± 3.6 | 20.4 ± 3.2 | 29.2 ± 3.6 | 20.9 ± 3.1 | 36 ± 4.8 | 18.1 ± 5.1 | 28.9 ± 4.9 | 16.9 ± 4.3 |
C. gallinacea 08-12743 | 31.3 ± 3.7 | 18.8 ± 3.2 | 30.3 ± 3.7 | 19.7 ± 3.5 | 39 ± 4.8 | 14.1 ± 4.8 | 31.6 ± 4.9 | 15.0 ± 4.6 |
C. avium 10DC88 | 31.7 ± 3.7 | 18.2 ± 3.0 | 30.9 ± 3.7 | 19.2 ± 3.3 | 40 ± 5.1 | 13.2 ± 4.4 | 32.8 ± 4.9 | 13.8 ± 4.2 |
C. felis Fe/C-56 | 30.1 ± 3.3 | 19.5 ± 2.7 | 29.9 ± 3.5 | 20.4 ± 2.9 | 37 ± 4.4 | 16.5 ± 4.1 | 30.4 ± 4.4 | 16.0 ± 3.9 |
C. caviae GPIC | 30.2 ± 3.4 | 19.3 ± 2.7 | 30.0 ± 3.5 | 20.5 ± 2.9 | 38 ± 4.5 | 16.0 ± 4.2 | 30.4 ± 4.5 | 15.8 ± 3.9 |
C. ibidis 10-1398 6 | 31.0 ± 3.7 | 18.5 ± 2.5 | 30.2 ± 3.6 | 20.3 ± 3.2 | 39 ± 4.8 | 14.5 ± 3.8 | 30.6 ± 5.0 | 15.7 ± 3.9 |
Strains | Correlation | Significance |
---|---|---|
C. trachomatis L2/25567R | r = 0.369 | p = 3.7 × 10−30 |
C. trachomatis A-Har-13 | r = 0.512 | p = 1.8 × 10−63 |
C. trachomatis ESW3 | r = 0.560 | p = 2.7 × 10−74 |
C. suis MD56 | r = 0.511 | p = 2.2 × 10−63 |
C. muridarum Nigg | r = 0.520 | p = 2.1 × 10−63 |
C. abortus S26/3 | r = 0.590 | p = 5.3 × 10−93 |
C. psittaci 6BC | r = 0.585 | p = 1.0 × 10−89 |
C. pecorum E58 | r = 0.554 | p = 2.8 × 10−79 |
C. pneumoniae TW-183 | r = 0.488 | p = 2.8 × 10−67 |
C. gallinacea 08-12743 | r = 0.548 | p = 1.6 × 10−71 |
C. avium 10DC88 | r = 0.630 | p = 1.3 × 10−104 |
C. felis Fe/C-56 | r = 0.580 | p = 4.5 × 10−89 |
C. caviae GPIC | r = 0.585 | p = 1.1 × 10−91 |
C. ibidis 10-1398/6 | r = 0.547 | p = 1.4 × 10−76 |
Strains | Correlation | Significance |
---|---|---|
C. trachomatis L2/25567R | r = 0.272 | p = 1.6 × 10−16 |
C. trachomatis A-Har-13 | r = −0.186 | p = 9.6 × 10−9 |
C. trachomatis ESW3 | r = −0.257 | p = 7.4 × 10−15 |
C. suis MD56 | r = −0.417 | p = 9.8 × 10−41 |
C. muridarum Nigg | r = −0.16 | p = 1.5 × 10−6 |
C. abortus S26/3 | r = −0.299 | p = 9.8 × 10−22 |
C. psittaci 6BC | r = −0.311 | p = 4.9 × 10−23 |
C. pecorum E58 | r = 0.005 | p = 0.882 |
C. pneumoniae TW-183 | r = −0.04 | p = 0.187 |
C. gallinacea 08-12743 | r = −0.168 | p = 4.0 × 10−7 |
C. avium 10DC88 | r = −0.308 | p = 5.4 × 10−22 |
C. felis Fe/C-56 | r = −0.268 | p = 1.4 × 10−17 |
C. caviae GPIC | r = −0.275 | p = 1.4 × 10−18 |
C. ibidis 10-1398/6 | r = −0.246 | p = 9.1 × 10−15 |
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Li, Z.; Hu, W.; Cao, X.; Liu, P.; Shang, Y.; Zhou, J. Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae. Int. J. Mol. Sci. 2018, 19, 4010. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms19124010
Li Z, Hu W, Cao X, Liu P, Shang Y, Zhou J. Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae. International Journal of Molecular Sciences. 2018; 19(12):4010. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms19124010
Chicago/Turabian StyleLi, Zhaocai, Wen Hu, Xiaoan Cao, Ping Liu, Youjun Shang, and Jizhang Zhou. 2018. "Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae" International Journal of Molecular Sciences 19, no. 12: 4010. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms19124010