Mutation pressure and natural selection on codon usage in chloroplast genes of two species in
            <i>Pisum</i>
            L. (Fabaceae: Faboideae)

Bhattacharyya, Debjyoti; Uddin, Arif; Das, Sudipta Kumar; Chakraborty, Supriyo

doi:10.1080/24701394.2019.1616701

Cited by 18 publications

(16 citation statements)

References 37 publications

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“…Chloroplast genomes of Asteracea family had a narrow GC distribution without significant correlation between GC12 and GC3, and purines were used more frequently than pyrimidines [93]. Natural selection might have played a prominent role over mutation pressure in sculpturing the CUB of chloroplast genes [94].…”

Section: Codon Usage In Nuclear and Organelle Genes Of Plantsmentioning

confidence: 99%

Codon usage bias

2021

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Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals. Different species have consistent and characteristic codon biases. Codon bias varies not only with species, family or group within kingdom, but also between the genes within an organism. Codon usage bias has evolved through mutation, natural selection, and genetic drift in various organisms. Genome composition, GC content, expression level and length of genes, position and context of codons in the genes, recombination rates, mRNA folding, and tRNA abundance and interactions are some factors influencing codon bias. The factors shaping codon bias may also be involved in evolution of the universal genetic code. Codon-usage bias is critical factor determining gene expression and cellular function by influencing diverse processes such as RNA processing, protein translation and protein folding. Codon usage bias reflects the origin, mutation patterns and evolution of the species or genes. Investigations of codon bias patterns in genomes can reveal phylogenetic relationships between organisms, horizontal gene transfers, molecular evolution of genes and identify selective forces that drive their evolution. Most important application of codon bias analysis is in the design of transgenes, to increase gene expression levels through codon optimization, for development of transgenic crops. The review gives an overview of deviations of genetic code, factors influencing codon usage or bias, codon usage bias of nuclear and organellar genes, computational methods to determine codon usage and the significance as well as applications of codon usage analysis in biological research, with emphasis on plants.

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Section: Codon Usage In Nuclear and Organelle Genes Of Plantsmentioning

confidence: 99%

Codon usage bias

2021

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“…Previous studies have found significant positive and negative correlations between GRAVY and AROMO values and codon usage bias in a variety of organisms, such as Pisum species [23], Ginkgo biloba [78], Oncidium Gower Ramsey [89], Epichloë festucae [77]. Finally, in the current study, I investigated the codon usage bias in the seven known lignan biosynthesis related genes and observed substantial differences in the codon usage among the lignan biosynthesis related genes.…”

Section: J O U R N a L P R E -P R O O F 12mentioning

confidence: 65%

“…CUB is also critical in shaping cellular function and gene expression through its effects that ranges from RNA processing to protein translation and protein folding [ 11 , 12 , 13 , 14 , 15 ]. There are several factors that have been suggested to affect codon usage bias, while mutational bias and selection for translation efficiency are considered as the two primary evolutionary forces with varying relative contribution among species [ 16 , 17 , 18 , 19 , 20 , 21 , 22 ]. Mutation is responsible to generate codon diversity while reduction of codon diversity is achieved mainly through natural selection.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of codon usage in sesame (Sesamum indicum L.)

Andargie

Zhu

2022

Heliyon

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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“…Neutrality plot analysis revealed that natural selection played a prominent role over mutation pressure in shaping the codon usage bias of chloroplast genes in two species of Pisum, viz. P. fulvum and P. sativum (Bhattacharyya et al, 2019), chloroplyll synthesis pathway-associated genes in monocot and dicot (Begum and Mondal, 2020), and Ginkgo biloba (He et al, 2016). The results of our neutrality plot indicated that natural selection played a pivotal role in determining the selective constraints on codon usage bias in the PQQ biosynthetic pathway-associated genes from selected Gammaproteobacteria.…”

Section: Neutrality Plot Analysismentioning

confidence: 78%

Study of Pyrroloquinoline Quinine From Phosphate-Solubilizing Microbes Responsible for Plant Growth: In silico Approach

et al. 2021

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Plants cannot uptake the insoluble form of phosphate from soil. Phosphate-solubilizing microbes (PSMs) release gluconic acid (C6H12O7) that is synthesized by the interaction between co-factor pyrroloquinoline quinine (PQQ) and glucose dehydrogenase within themselves and hence convert the insoluble phosphate into a soluble form. Phylogenetic analyses based on individual sequences of PqqA–PqqE proteins involved in the PQQ biosynthetic pathway manifested clear clustering formation of the selected species according to their respective genera such as Pantoea, Rouxiella, Rahnella, Kosakonia, Mixta, Cronobacter, and Serratia. In multiple sequence alignment (MSA), numerous semi-conserved sites were identified that indicate acquired mutation during evolution. The selected pqq genes that appeared within an operon system sustain a specified order viz. pqqABCDE for both positive and negative strands. The nucleotide composition of the encoding genes displayed higher content of GCs at different positions of the codons and has also been properly reflected in relative synonymous codon usage (RSCU) values of the codons with few exceptions. The correspondence analysis (COA) based on RSCU proclaimed that the pqqB genes prefer A/U-ending codons over G/C, while for the pqqE gene, G/C-ending codons are comparatively more preferable (except CGU). Mutational pressure contributes to shaping the codon usage pattern for the selected pqq genes evinced from the COAs, while the ENc and neutrality plot gives attestation of natural selection. The higher values of CAI indicate the gene adaptability and codon usage bias. These comprehensive computational studies can be beneficial for further research in molecular phylogenetics, genomics, and proteomics and to better understand the evolutionary dynamics of PQQ.

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Mutation pressure and natural selection on codon usage in chloroplast genes of two species in Pisum L. (Fabaceae: Faboideae)

Cited by 18 publications

References 37 publications

Codon usage bias

Codon usage bias

Genome-wide analysis of codon usage in sesame (Sesamum indicum L.)

Study of Pyrroloquinoline Quinine From Phosphate-Solubilizing Microbes Responsible for Plant Growth: In silico Approach

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