ArticlePloS one2012
Mutational bias and translational selection shaping the codon usage pattern of tissue-specific genes in rice.
Article in PloS one, 2012. 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.
- Repetitive Sequences, Codon Usage Bias and Phylogenetic Analysis of the Plastome of Miliusa glochidioides.Biochemical genetics · 2025Article
- Novel findings on the mitochondria in ciliates, with description of mitochondrial genomes of six representatives.Marine life science & technology · 2025Article
- Correlations of gene expression, codon usage bias, and evolutionary rates of the mitochondrial genome show tissue differentiation in Ophioglossum vulgatum.BMC plant biology · 2025Article
- In silico methods for predicting functional synonymous variants.Genome biology · 2023Review
- Mutational Bias and Natural Selection Driving the Synonymous Codon Usage of Single-Exon Genes in Rice (Oryza sativa L.).Rice (New York, N.Y.) · 2023Article
- Composition and Codon Usage Pattern Results in Divergence of theJournal of fungi (Basel, Switzerland) · 2022Article
- The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.NAR genomics and bioinformatics · 2022Article
- Distinct responses to rare codons in selecteLife · 2022Article
- Codon usage bias.Molecular biology reports · 2022Review
- Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues.BMC genomics · 2021Article
- Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes.BMC genomics · 2021Article
- Cost-efficiency tradeoff is optimized in various cancer types revealed by genome-wide analysis.Molecular genetics and genomics : MGG · 2021Article
- MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life.Nucleic acids research · 2020Article
- Evidence of multifaceted functions of codon usage in translation within the model beetle Tribolium castaneum.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster.Genome biology and evolution · 2019Article
- Article
- Codon usage and codon pair patterns in non-grass monocot genomes.Annals of botany · 2017Review
- New insights into the interplay between codon bias determinants in plants.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Asymmetric Context-Dependent Mutation Patterns Revealed through Mutation-Accumulation Experiments.Molecular biology and evolution · 2015Article
- Mutational bias is the driving force for shaping the synonymous codon usage pattern of alternatively spliced genes in rice (Oryza sativa L.).Molecular genetics and genomics : MGG · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The regulatory mechanisms of determining which genes specifically expressed in which tissues are still not fully elucidated, especially in plants. Using internal correspondence analysis, I first establish that tissue-specific genes exhibit significantly different synonymous codon usage in rice, although this effect is weak. The variability of synonymous codon usage between tissues accounts for 5.62% of the total codon usage variability, which has mainly arisen from the neutral evolutionary forces, such as GC content variation among tissues. Moreover, tissue-specific genes are under differential selective constraints, inferring that natural selection also contributes to the codon usage divergence between tissues. These findings may add further evidence in understanding the differentiation and regulation of tissue-specific gene products in plants.
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.