ArticleBMC evolutionary biology2009
Codon usage is associated with the evolutionary age of genes in metazoan genomes.
Article in BMC evolutionary biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 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
36 citing papers in PubMed, 80 citations in OpenAlex.
- A previously unrecognized class of fungal ice-nucleating proteins with bacterial ancestry.Science advances · 2026Article
- Mapping the inter- and intra-genic codon-usage landscape inNAR genomics and bioinformatics · 2026Article
- Comparative mitogenomics reveals evolutionary drivers of Strongyloidea nematodes dwelling in gastrointestinal tract.BMC genomics · 2025Article
- Article
- Codon-Usage Bias and Genomic Architecture of 79 Psoriasis-Susceptibility Genes: Implications for Expression Efficiency and Therapeutic Targeting.Psoriasis (Auckland, N.Z.) · 2025Article
- Description of mitochondrial genomes and phylogenetic analysis of Megophthalminae (Hemiptera: Cicadellidae).Journal of insect science (Online) · 2024Article
- Phylogenomics and plastome evolution of Lithospermeae (Boraginaceae).BMC plant biology · 2024Article
- Dynamic evolution of peste des petits ruminants virus in sheep and goat hosts across India reveals the swift surge of F gene.Virusdisease · 2024Article
- Codon Optimization Improves the Prediction of Xylose Metabolism from Gene Content in Budding Yeasts.Molecular biology and evolution · 2023Article
- Article
- The evolutionary and molecular features of the broad-host-range plant pathogen Sclerotinia sclerotiorum.Molecular plant pathology · 2022Review
- Codon usage patterns across seven Rosales species.BMC plant biology · 2022Article
- Genome-wide analysis of codon usage in sesame (Heliyon · 2022Article
- Analysis of Codon Usage Patterns inGenes · 2021Article
- The whale shark genome reveals how genomic and physiological properties scale with body size.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Compositional properties and codon usage pattern of mitochondrial ATP gene in different classes of Arthropoda.Genetica · 2019Article
- Article
- Article
- Toward Reducing Phylostratigraphic Errors and Biases.Genome biology and evolution · 2018Article
- Codon usage vis-a-vis start and stop codon context analysis of three dicot species.Journal of genetics · 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 at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCodon usage may vary significantly between different organisms and between genes within the same organism. Several evolutionary processes have been postulated to be the predominant determinants of codon usage: selection, mutation, and genetic drift. However, the relative contribution of each of these factors in different species remains debatable. The availability of complete genomes for tens of multicellular organisms provides an opportunity to inspect the relationship between codon usage and the evolutionary age of genes.
resultsWe assign an evolutionary age to a gene based on the relative positions of its identified homologues in a standard phylogenetic tree. This yields a classification of all genes in a genome to several evolutionary age classes. The present study starts from the observation that each age class of genes has a unique codon usage and proceeds to provide a quantitative analysis of the codon usage in these classes. This observation is made for the genomes of Homo sapiens, Mus musculus, and Drosophila melanogaster. It is even more remarkable that the differences between codon usages in different age groups exhibit similar and consistent behavior in various organisms. While we find that GC content and gene length are also associated with the evolutionary age of genes, they can provide only a partial explanation for the observed codon usage.
conclusionWhile factors such as GC content, mutational bias, and selection shape the codon usage in a genome, the evolutionary history of an organism over hundreds of millions of years is an overlooked property that is strongly linked to GC content, protein length, and, even more significantly, to the codon usage of metazoan 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.