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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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Start codon-associated ribosomal frameshifting mediates nutrient stress adaptation
A translating ribosome is typically thought to follow the reading frame defined by the selected start codon. Using super-resolution ribosome...
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Analysis of chloroplast genome characteristics and codon usage bias in 14 species of Annonaceae
For the study of species evolution, chloroplast gene expression, and transformation, the chloroplast genome is an invaluable resource. Codon usage...
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Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae
Rutaceae family comprises economically important plants due to their extensive applications in spices, food, oil, medicine, etc. The Rutaceae plants...
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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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Compositional Dynamics and Codon Usage Pattern of Myogenin (MyoG) Gene across Different Mammalian Species
AbstractMyoG enin ( MyoG ) is one of the key regulatory factors for controlling the generation of skeletal muscle. Codon usage bias (CUB) as a unique...
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Analysis of codon usage patterns in 48 Aconitum species
BackgroundThe Aconitum genus is a crucial member of the Ranunculaceae family. There are 350 Aconitum species worldwide, with about 170 species found...
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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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SARS-CoV-2 continuously optimizes its codon usage to adapt to human lung environment
Viruses need to utilize the resources from host cells to reproduce themselves. RNA translation rate, which is largely determined by codon usage, is...
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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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Using protein-per-mRNA differences among human tissues in codon optimization
BackgroundCodon usage and nucleotide composition of coding sequences have profound effects on protein expression. However, while it is recognized...
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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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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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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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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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Codon usage bias analysis of mitochondrial protein-coding genes in 12 species of Candida
The incidence of diseases that are caused by fungal infection is gradually increasing, together with antibiotic abuse and the number of patients with...
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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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Adaption of tobacco rattle virus to its solanaceous hosts is related to the codon usage bias of the hosts and that of the viral 16 K gene
Tobacco rattle virus (TRV) is a member of the genus Tobravirus , family Virgaviridae , that infects many different plants from 50 families. TRV-based...
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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...
