ArticleEvolutionary bioinformatics online2013
Analysis of synonymous codon usage patterns in seven different citrus species.
Article in Evolutionary bioinformatics online, 2013. 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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15 citing papers in PubMed.
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- Comparative Genomics, Phylogenetics, Biogeography, and Effects of Climate Change onPlants (Basel, Switzerland) · 2022Article
- Codon usage bias.Molecular biology reports · 2022Review
- A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses.Gene reports · 2021Article
- Engineering a Plant-Derived Astaxanthin Synthetic Pathway IntoFrontiers in plant science · 2021Article
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- The Complete Chloroplast Genomes ofInternational journal of molecular sciences · 2019Article
- Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus.International journal of molecular sciences · 2019Article
- Comparative Genomic Analysis of Soil Dwelling Bacteria Utilizing a Combinational Codon Usage and Molecular Phylogenetic Approach Accentuating on Key Housekeeping Genes.Frontiers in microbiology · 2019Article
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- Codon usage and codon pair patterns in non-grass monocot genomes.Annals of botany · 2017Review
- Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Compensating the Fitness Costs of Synonymous Mutations.Molecular biology and evolution · 2016Article
- Gene Evolutionary Trajectories and GC Patterns Driven by Recombination inFrontiers in plant science · 2016Article
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6 authors.
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Abstract
We used large samples of expressed sequence tags to characterize the patterns of codon usage bias (CUB) in seven different Citrus species and to analyze their evolutionary effect on selection and base composition. We found that A- and T-ending codons are predominant in Citrus species. Next, we identified 21 codons for 18 different amino acids that were considered preferred codons in all seven species. We then performed correspondence analysis and constructed plots for the effective number of codons (ENCs) to analyze synonymous codon usage. Multiple regression analysis showed that gene expression in each species had a constant influence on the frequency of optional codons (FOP). Base composition differences between the proportions were large. Finally, positive selection was detected during the evolutionary process of the different Citrus species. Overall, our results suggest that codon usages were the result of positive selection. Codon usage variation among Citrus genes is influenced by translational selection, mutational bias, and gene length. CUB is strongly affected by selection pressure at the translational level, and gene length plays only a minor role. One possible explanation for this is that the selection-mediated codon bias is consistently strong in Citrus, which is one of the most widely cultivated fruit trees.
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