ArticleFrontiers in microbiology2016
Pangenome Evidence for Higher Codon Usage Bias and Stronger Translational Selection in Core Genes of Escherichia coli.
Article in Frontiers in microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Genomic and physiological signatures of adaptation in pathogenic fungi.Nature communications · 2026Article
- The genomic configurations driving antimicrobial resistance and virulence in colistin resistant Pseudomonas aeruginosa from an Egyptian Tertiary Oncology Hospital.PLOS global public health · 2025Article
- DNA Segregation in Enterobacteria.EcoSal Plus · 2023Review
- Synonymous sites for accessibility around microRNA binding sites in bacterial spot and speck disease resistance genes of tomato.Functional & integrative genomics · 2023Article
- A Study on microRNAs Targeting the Genes Overexpressed in Lung Cancer and their Codon Usage Patterns.Molecular biotechnology · 2022Article
- Whole genome sequencing and comparative genomic analyses of Pseudomonas aeruginosa strain isolated from arable soil reveal novel insights into heavy metal resistance and codon biology.Current genetics · 2022Article
- Distinguishing Pathovars from Nonpathovars: Escherichia coli.Microbiology spectrum · 2020Review
- Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes.Frontiers in microbiology · 2019Article
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Authors and funding
4 authors.
Funding
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Abstract
Codon usage bias, as a combined interplay from mutation and selection, has been intensively studied in Escherichia coli. However, codon usage analysis in an E. coli pangenome remains unexplored and the relative importance of mutation and selection acting on core genes and strain-specific genes is unknown. Here we perform comprehensive codon usage analyses based on a collection of multiple complete genome sequences of E. coli. Our results show that core genes that are present in all strains have higher codon usage bias than strain-specific genes that are unique to single strains. We further explore the forces in influencing codon usage and investigate the difference of the major force between core and strain-specific genes. Our results demonstrate that although mutation may exert genome-wide influences on codon usage acting similarly in different gene sets, selection dominates as an important force to shape biased codon usage as genes are present in an increased number of strains. Together, our results provide important insights for better understanding genome plasticity and complexity as well as evolutionary mechanisms behind codon usage bias.
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