ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2013
Evaluation of codon biology in citrus and Poncirus trifoliata based on genomic features and frame corrected expressed sequence tags.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed.
- Mitochondrial genomes of Dactylogyrus wunderi (Monopisthocotyla: Dactylogyridae): structural features, codon usage patterns, and phylogenetic implications.BMC genomics · 2026Article
- Mitochondrial Genome ofAnimals : an open access journal from MDPI · 2026Article
- Comprehensive Codon Usage Analysis Across Diverse Plant Lineages.Biochemical genetics · 2026Article
- Differentiation and validation of mild and severe strains of citrus tristeza virus through codon usage bias, host adaptation, and biochemical profiling.Frontiers in microbiology · 2025Article
- Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species.BMC genomic data · 2023Article
- Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus.BMC genomic data · 2022Article
- Codon usage patterns across seven Rosales species.BMC plant biology · 2022Article
- Article
- Codon usage bias.Molecular biology reports · 2022Review
- Analysis of codon usage bias of classical swine fever virus.Veterinary world · 2021Article
- Engineering a Plant-Derived Astaxanthin Synthetic Pathway IntoFrontiers in plant science · 2021Article
- Analysis of codon usage patterns in citrus based on coding sequence data.BMC genomics · 2020Article
- Codon Usage Bias Analysis ofViruses · 2019Article
- Evidence-based gene models for structural and functional annotations of the oil palm genome.Biology direct · 2017Article
- The Evolutionary Basis of Translational Accuracy in Plants.G3 (Bethesda, Md.) · 2017Article
- ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data.BMC bioinformatics · 2017Article
- The complete chloroplast genome sequence ofPeerJ · 2017Article
- The mysterious orphans of Mycoplasmataceae.Biology direct · 2016Article
- 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
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of Citrus species and P. trifoliata. The present study postulates a large repertoire of a set of optimal codons for the Citrus genus and P. trifoliata and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in Citrus and P. trifoliata. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (∼10.96%) of the recorded variance. In all analysed species, except P. trifoliata, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in Citrus species and P. trifoliata. Our present analysis postulates compositional constraints in Citrus species and P. trifoliata and plausible role of the stress with GC3 and coevolution pattern of amino acid.
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.