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Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae
Zhaocai Li1, Wen Hu2,3, Xiaoan Cao4
1State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China. lizhaocai@caas.cn.
International Journal of Molecular Sciences
|December 15, 2018
Summary
Chlamydia bacteria exhibit A/T-rich genes, influencing codon usage and dividing species into distinct evolutionary clusters. Mutation pressure significantly shapes these synonymous codon usage patterns in Chlamydiaceae.
Area of Science:
- Microbiology
- Evolutionary Biology
- Genomics
Background:
- Chlamydiaceae are obligate intracellular bacteria with diverse hosts.
- Understanding their evolutionary trends is crucial for pathogen cross-infection insights.
Purpose of the Study:
- Investigate nucleotide, codon, and amino acid usage bias in 12 Chlamydia species.
- Analyze evolutionary patterns within the Chlamydiaceae family.
Main Methods:
- Whole genome analysis of 14 Chlamydia genomes.
- Synonymous codon usage value and information entropy methods.
- Effective number of codons (ENC) and codon adaptation index (CAI) calculations.
Main Results:
- All studied Chlamydia species show A/T-rich genes with biased nucleotide composition.
- Codon usage divides Chlamydia into four clusters; amino acid usage into two.
- ENC positively correlates with gene GC3 content, suggesting mutation pressure influences codon usage.
Conclusions:
- Nucleotide composition and mutation pressure are key drivers of codon usage patterns in Chlamydiaceae.
- Codon usage of T3ss and Pmp gene families aligns with their respective genomes.
- Study enhances understanding of evolutionary interactions in Chlamydiaceae genes.
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