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Selection of start codon during mRNA scanning in eukaryotic translation initiation
Accurate and high-speed scanning and subsequent selection of the correct start codon are important events in protein synthesis. Eukaryotic mRNAs have...
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Translation Comes First: Ancient and Convergent Selection of Codon Usage Bias Across Prokaryotic Genomes
Codon usage is the outcome of different evolutionary processes and can inform us about the conditions in which organisms live and evolve. Here, we...
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Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach
BackgroundCodon usage bias (CUB), the non-uniform usage of synonymous codons, occurs across all domains of life. Adaptive CUB is hypothesized to...
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Context-Dependent Mutation Dynamics, Not Selection, Explains the Codon Usage Bias of Most Angiosperm Chloroplast Genes
Two competing proposals about the degree to which selection affects codon usage of angiosperm chloroplast genes are examined. The first, based on...
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ICOR: improving codon optimization with recurrent neural networks
BackgroundIn protein sequences—as there are 61 sense codons but only 20 standard amino acids—most amino acids are encoded by more than one codon....
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Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species
Gracilariaceae is a group of marine large red algae and main source of agar with important economic and ecological value. The codon usage patterns of...
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Codon usage pattern of the ancestor of green plants revealed through Rhodophyta
Rhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern...
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An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea
BackgroundThe chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant...
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Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains
In this study, we investigated the codon bias of twelve mitochondrial core protein coding genes (PCGs) in eight Pleurotus strains, two of which are...
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Comparative analysis of codon usage patterns in the chloroplast genomes of nine forage legumes
Leguminosae is one of the three largest families of angiosperms after Compositae and Orchidaceae . It is widely distributed and grows in a variety of...
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Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina
BackgroundHemerocallis citrina Baroni is a traditional vegetable crop widely cultivated in eastern Asia for its high edible, medicinal, and...
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Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species
BackgroundThe Phenomenon of codon usage bias exists in the genomes of prokaryotes and eukaryotes. The codon usage pattern is affected by...
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Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis
Codon and amino acid usage were associated with almost every aspect of microbial life. However, how the environment may impact the codon and amino...
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Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming
Cancers commonly reprogram translation and metabolism, but little is known about how these two features coordinate in cancer stem cells. Here we show...
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Codon usage bias
Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals....
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Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus
BackgroundKuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus...
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An investigation of codon usage pattern analysis in pancreatitis associated genes
BackgroundPancreatitis is an inflammatory disorder resulting from the autoactivation of trypsinogen in the pancreas. The genetic basis of the disease...
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Codon usage bias and genetic diversity in chloroplast genomes of Elaeagnus species (Myrtiflorae: Elaeagnaceae)
Codon usage bias (CUB) reveals the characteristics of species and can be utilized to understand their evolutionary relationship, increase the target...
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Codon usage bias and evolution analysis in the mitochondrial genome of Mesona chinensis Benth
Mesona chinensis Benth (MCB) is an edible and medicinal plant in southern China and Southeast Asian countries. Mitochondria, semi-autonomous...
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Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus
BackgroundThe phenomenon of codon usage bias is known to exist in many genomes and is mainly determined by mutation and selection. Codon usage bias...
