Codon usage bias

Parvathy, S.; Udayasuriyan, V.; Bhadana, V. P.

doi:10.1007/s11033-021-06749-4

Cited by 202 publications

(164 citation statements)

References 118 publications

Supporting

Mentioning

119

Contrasting

Unclassified

Order By: Relevance

“…The values in the graph represent the total number of interactions between each protein-coding gene and others in the protein–protein network. Codon bias. Codon usage bias is the preferential or nonrandom use of synonymous codes, a common phenomenon observed in bacteria, plants, and animals . A total of 4302 CDS-type E.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

EcoliGD: An Online Tool for Designing Escherichia coli Genome

et al. 2022

View full text Add to dashboard Cite

Synthetic biology is an important interdisciplinary field that has emerged in this century, focusing on the rewriting and reprogramming of DNA through the cycles of “design-edit”, and so, the cell’s own operating system, its genome, is naturally coming into focus. Here, we propose EcoliGD, an online genome design tool with a visual interactive interface and the function of browsing information, as well as the ability to perform insertion, exchange, deletion, and codon replacement operations on the E. coli genome and display the results in real-time. Users can utilize EcoliGD to check various functional characteristic about E. coli genes, to help them build their genomes. Furthermore, we also collected experimentally verified large genomic segments that have been successfully deleted from the genome for users to choose from and simplify the genome. EcoliGD can help recode the entire E. coli genome, providing a novel way to explore the diversity and function of this microorganism. The EcoliGD web tool is available at .

show abstract

Section: Resultsmentioning

confidence: 99%

“…Codon bias. Codon usage bias is the preferential or nonrandom use of synonymous codes, a common phenomenon observed in bacteria, plants, and animals . A total of 4302 CDS-type E.…”

Section: Resultsmentioning

confidence: 99%

EcoliGD: An Online Tool for Designing Escherichia coli Genome

et al. 2022

View full text Add to dashboard Cite

show abstract

“…In addition, codon usage bias (CUB), referring to the unbalanced utilization of synonymous codons in coding DNA, can be analyzed for getting insights into the evolutionary patterns of both taxa and genes [ 34 , 35 , 36 , 37 , 38 ]. By the statistical analysis of CUB, we can speculate which factor is mainly responsible for bias pattern, usually mutational bias or natural selection [ 39 , 40 , 41 ].…”

Section: Introductionmentioning

confidence: 99%

Plastomes of Bletilla (Orchidaceae) and Phylogenetic Implications

Han¹,

Wang

Hong

et al. 2022

IJMS

View full text Add to dashboard Cite

The genus Bletilla is a small genus of only five species distributed across Asia, including B. chartacea, B. foliosa, B. formosana, B. ochracea and B. striata, which is of great medicinal importance. Furthermore, this genus is a member of the key tribe Arethuseae (Orchidaceae), harboring an extremely complicated taxonomic history. Recently, the monophyletic status of Bletilla has been challenged, and the phylogenetic relationships within this genus are still unclear. The plastome, which is rich in both sequence and structural variation, has emerged as a powerful tool for understanding plant evolution. Along with four new plastomes, this work is committed to exploring plastomic markers to elucidate the phylogeny of Bletilla. Our results reveal considerable plastomic differences between B. sinensis and the other three taxa in many aspects. Most importantly, the specific features of the IR junction patterns, novel pttRNA structures and codon aversion motifs can serve as useful molecular markers for Bletilla phylogeny. Moreover, based on maximum likelihood and Bayesian inference methods, our phylogenetic analyses based on two datasets of Arethuseae strongly imply that Bletilla is non-monophyletic. Accordingly, our findings from this study provide novel potential markers for species identification, and shed light on the evolution of Bletilla and Arethuseae.

show abstract

“…Even though they encode the same amino acid, it has been shown for all organisms that there is unequal occurrence of synonymous codons in a genome, a phenomenon called codon usage bias (CUB) (Behura and Severson 2013). The major factors in uencing CUB are genetic drift, mutation pressure and natural selection (Salim and Cavalcanti 2008;Nath Choudhury et al 2017;Gun et al 2018;Parvathy et al 2022). Therefore, when studied in details, CUB echoes the origin of mutation pattern as well as evolution of species or genes, and can help to categorize a gene (or species) and interpret its evolutionary trends.…”

Section: Introductionmentioning

confidence: 99%

Compositional properties and codon usage pattern of mitochondrial cytochrome c oxidase I gene among Potamidids

Shabani

Mfilinge

Mpenda

2022

Preprint

View full text Add to dashboard Cite

Codon usage bias refers to the phenomenon where there is unequal occurrence of specific synonymous codons in a genome, the frequency of which varies within and among species. Molecular evolutionary researches suggest that CUB studies are significant in interpreting evolutionary trends of species or genes. A number of studies on codon usage bias are emerging in different organisms. However, such information remained unclear for organisms in the family Potamididae. This study systematically examined compositional features and codon usage patterns in MT-COI gene among potamidids to identify factors shaping codon usage bias. Quantification of codon usage bias and the identification of causative factors was performed by assessing various parameters such as nucleotide composition, effective number of codons (ENC), relative synonymous codon usage (RSCU), parity rule (PR2) analysis, neutrality plot analysis as well as a multivariate statistical approach of correspondence analysis (CoA). The results from neutrality plot suggested that natural selection is the dominant evolutionary factor for CUB in MT-COI gene among the different genera of potamidids. Correspondence analysis (CoA), parity plot and ENC analyses indicated the existence of mutational pressure with minor contribution. Nucleotide composition investigations indicated that, most codons are AT rich, with T nucleotides count being highly presented. Thus, compositional restraint was shown as among the reasons behind the pattern of codon usage in MT-COI gene of species in the family Potamididae.

show abstract

Codon usage bias

Cited by 202 publications

References 118 publications

EcoliGD: An Online Tool for Designing Escherichia coli Genome

EcoliGD: An Online Tool for Designing Escherichia coli Genome

Plastomes of Bletilla (Orchidaceae) and Phylogenetic Implications

Compositional properties and codon usage pattern of mitochondrial cytochrome c oxidase I gene among Potamidids

Contact Info

Product

Resources

About