ArticlePloS one2014
Analysis of the relationship between genomic GC Content and patterns of base usage, codon usage and amino acid usage in prokaryotes: similar GC content adopts similar compositional frequencies regardless of the phylogenetic lineages.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed.
- A previously unrecognized class of fungal ice-nucleating proteins with bacterial ancestry.Science advances · 2026Article
- Contrasting genome composition and codon usage inVirus evolution · 2026Article
- Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage.Journal of molecular evolution · 2025Article
- Molecular phylogenetic relationships based on chloroplast genomes of Zingiberaceae species: Insights into evolution and adaptation to extreme environments.Frontiers in plant science · 2025Article
- Comparative Analysis of the Codon Usage Pattern in the Chloroplast Genomes of Gnetales Species.International journal of molecular sciences · 2024Article
- Complete organelle genomes of the threatened aquatic speciesEcology and evolution · 2024Article
- A computational approach to developing a multi-epitope vaccine for combating Pseudomonas aeruginosa-induced pneumonia and sepsis.Briefings in bioinformatics · 2024Article
- Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa.Microorganisms · 2023Article
- Genomic Characterization of Carbapenem-Resistant Bacteria from Beef Cattle Feedlots.Antibiotics (Basel, Switzerland) · 2023Article
- Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis.NPJ biofilms and microbiomes · 2023Article
- The effect of the genomic GC content bias of prokaryotic organisms on the secondary structures of their proteins.PloS one · 2023Article
- The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.NAR genomics and bioinformatics · 2022Article
- An overview of dinucleotide and codon usage in all viruses.Archives of virology · 2022Review
- Designing of peptide aptamer targeting the receptor-binding domain of spike protein of SARS-CoV-2: an in silico study.Molecular diversity · 2022Article
- T-G-A Deficiency Pattern in Protein-Coding Genes and Its Potential Reason.Frontiers in microbiology · 2022Article
- Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts.Frontiers in microbiology · 2021Article
- CUBAP: an interactive web portal for analyzing codon usage biases across populations.Nucleic acids research · 2020Article
- Draft Genome Sequence of Bacillus safensis Strain Sami, Isolated from Leaf Veins ofMicrobiology resource announcements · 2019Article
- Comprehensive profiling of codon usage signatures and codon context variations in the genus Ustilago.World journal of microbiology & biotechnology · 2019Article
- Amino acid compositions contribute to the proteins' evolution under the influence of their abundances and genomic GC content.Scientific reports · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The GC contents of 2670 prokaryotic genomes that belong to diverse phylogenetic lineages were analyzed in this paper. These genomes had GC contents that ranged from 13.5% to 74.9%. We analyzed the distance of base frequencies at the three codon positions, codon frequencies, and amino acid compositions across genomes with respect to the differences in the GC content of these prokaryotic species. We found that although the phylogenetic lineages were remote among some species, a similar genomic GC content forced them to adopt similar base usage patterns at the three codon positions, codon usage patterns, and amino acid usage patterns. Our work demonstrates that in prokaryotic genomes: a) base usage, codon usage, and amino acid usage change with GC content with a linear correlation; b) the distance of each usage has a linear correlation with the GC content difference; and c) GC content is more essential than phylogenetic lineage in determining base usage, codon usage, and amino acid usage. This work is exceptional in that we adopted intuitively graphic methods for all analyses, and we used these analyses to examine as many as 2670 prokaryotes. We hope that this work is helpful for understanding common features in the organization of microbial genomes.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.