ArticlemBio2020
Codon Usage Optimization in the Prokaryotic Tree of Life: How Synonymous Codons Are Differentially Selected in Sequence Domains with Different Expression Levels and Degrees of Conservation.
Article in mBio, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 21 citations in OpenAlex.
- PyamilySeq: exposing the fragility of conventional gene (re)clustering and prokaryotic pangenomic inference methods.NAR genomics and bioinformatics · 2026Article
- Codon usage optimization contributes to evolutionary dynamics of TetM following its acquisition via interspecies and intergeneric recombination events in recipient bacteria.BMC microbiology · 2026Article
- Stable association of a chlamydial symbiont with the freshwater predator hydra suggests broad host potential.The ISME journal · 2026Article
- tRNA Modification Landscapes in Streptococci: Shared Losses and Clade-Specific Adaptations.bioRxiv : the preprint server for biology · 2025Article
- Article
- Molecular epidemiology and genetic dynamics of carbapenem-resistant hypervirulentFrontiers in cellular and infection microbiology · 2025Article
- The fitness connection of antibiotic resistance.Frontiers in microbiology · 2025Article
- Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.Current genomics · 2025Review
- Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains.BMC genomics · 2024Article
- Impact of the chemical modification of tRNAs anticodon loop on the variability and evolution of codon usage in proteobacteria.Frontiers in microbiology · 2024Article
- Growth-dependent Gene Expression Variation Influences the Strength of Codon Usage Biases.Molecular biology and evolution · 2023Article
- Growth rate is a dominant factor predicting the rhizosphere effect.The ISME journal · 2023Article
- Growth-dependent gene expression variation influences the strength of codon usage biases.bioRxiv : the preprint server for biology · 2023Article
- Comprehensive analysis of codon bias in 13Frontiers in microbiology · 2023Article
- The Dynamic Codon Biaser: calculating prokaryotic codon usage biases.Microbial genomics · 2021Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prokaryote genomes exhibit a wide range of GC contents and codon usages, both resulting from an interaction between mutational bias and natural selection. In order to investigate the basis underlying specific codon changes, we performed a comprehensive analysis of 29 different prokaryote families. The analysis of core gene sets with increasing ancestries in each family lineage revealed that the codon usages became progressively more adapted to the tRNA pools. While, as previously reported, highly expressed genes presented the most optimized codon usage, the singletons contained the less selectively favored codons. The results showed that usually codons with the highest translational adaptation were preferentially enriched. In agreement with previous reports, a C bias in 2- to 3-fold pyrimidine-ending codons, and a U bias in 4-fold codons occurred in all families, irrespective of the global genomic GC content. Furthermore, the U biases suggested that U
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.