Mutational Pressure Drives Evolution of Synonymous Codon Usage in Genetically Distinct Oenothera plastomes

Rahul, R Nair; Nimal, T Raveendran; Dirisala, Vijaya R.; Manivasagam, B Nandhini; Sethuraman, Thilaga; Thirupati, Chinna Venkateswarulu; Ganesh, D.

doi:10.15171/ijb.1156

Cited by 6 publications

(6 citation statements)

References 53 publications

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“…Genes with low expression levels have high ENc values and more rare codons 32 . The expression of highly biased genes is considered as high 33 . The relative expression can be concluded from the ENc value, where small ENc value indicates higher bias and a generally higher level of expression 34 .…”

Section: Discussionmentioning

confidence: 99%

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From SARS and MERS CoVs to SARS‐CoV‐2: Moving toward more biased codon usage in viral structural and nonstructural genes

Kandeel

Ibrahim

Fayez

et al. 2020

Journal of Medical Virology

176

139

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Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS-CoV-2 and the changes in SARS-CoV-2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses. Methods: The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA-dependent RNA polymerase and main protease (Mpro) of SARS-CoV-2, Beta-CoV from pangolins, bat SARS, MERS, and SARS CoVs. Results: SARS-CoV-2 prefers pyrimidine rich codons to purines. Most highfrequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS-CoV-2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS-CoV-2 structural proteins. SARS-CoV-2 encoded the highest number of over-biased and negatively biased codons. Pangolin Beta-CoV showed little differences with SARS-CoV-2 ENc values, compared with SARS, bat SARS, and MERS CoV. Conclusion: Extreme bias and lower ENc values of SARS-CoV-2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs.

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Section: Discussionmentioning

confidence: 99%

“…32 The expression of highly biased genes is considered as high. 33 The relative expression can be concluded from the ENc value, where small ENc value indicates higher bias and a generally higher level of expression. 34 Thus, the small ENc value is suggesting for higher gene expression.…”

Section: Discussionmentioning

confidence: 99%

From SARS and MERS CoVs to SARS‐CoV‐2: Moving toward more biased codon usage in viral structural and nonstructural genes

Kandeel

Ibrahim

Fayez

et al. 2020

Journal of Medical Virology

176

139

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“…As Fop, CAI and CBI indices use specific reference gene sets, they provide a measure of bias towards particular codons that appear to be translationally optimal in that species (Behura and Severson, 2013). Among these indices, use of CAI is most widely reported, for example in codon usage analysis of Oenothera (Nair et al, 2014) and G. biloba (He et al, 2016), while Fop has been applied in studies for Picea (De La Torre et al, 2015) and Medicago truncatula (Song et al, 2015). As CAI values are determined from reference sets of highly expressed genes, which may be different among species, the relative fitness values of the species will also be different.…”

Section: Tools and Indices For Assessing Codon Usagementioning

confidence: 99%

“…Euclidean measurements of distance between the genes and the codon frequencies are estimated and the values plotted to visually indicate the association of genes to a particular codon and their similarities with other genes (Perrière and Thioulouse, 2002). Examples of cluster analysis applied to plant species include studies of the codon usage of protein coding sequences in G. biloba (He et al, 2016), herbaceous peony (Paeonia lactiflora) (Wu et al, 2015), citrus species (Xu et al, 2013), the chloroplast genome of Oenothera (Nair et al, 2014) and the mitochondrial genomes of wheat (Triticum aestivum), maize (Zea mays), Arabidopsis thaliana, tobacco (Nicotiana tabacum), Physcomitrella patens and Marchantia polymorpha (Zhou and Li, 2009). Cluster analyses have also been used to classify and categorize codon usage in various plant genomes (Ma et al, 2015;Priya et al, 2016), but in a few cases, the method did not accurately reflect the phylogenetic relationships among plants (Nair et al, 2014;You et al, 2015).…”

Section: Tools and Indices For Assessing Codon Usagementioning

confidence: 99%

Codon usage and codon pair patterns in non-grass monocot genomes

et al. 2017

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“…32 Two data sets for a 2 × 2 matrix were developed by selecting 10% of the genes that were grouped on the left and the right extremes of the first axis of the correspondence analysis (COA). 33,34 Observed frequencies of codons in the two data sets are given in the first row and the total number of synonymous alternatives of that given codon is given in the second row of the 2 × 2 matrix. 30 Level of significance was measured at P , 0.05. codon adaptation index.…”

Section: Methodsmentioning

confidence: 99%

Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha

Karumathil¹,

Dirisala

Srinadh

et al. 2016

Bioinform Biol Insights

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Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed. Spearman’s rank correlation analyses of nucleotide contents suggested that mutational pressure and selection were acting in all examined mitogenomes but with varying intensities. The quantification of SCUB using effective number of codons vs. GC composition at the third codon position (GC3) plot suggested that mutational pressure due to GC compositional constraints might be one of the major influencing forces driving the SCUB in all chaetognaths except Sagitta enflata. However, neutrality plots revealed no significant correlation between GC3 and cumulative GC content at first and second codon positions (GC12) in all other species, except in Daphnia pulex. The parity rule 2 bias plot showed that significant compositional differences existed between C and G, as well as between A and T, contents in most of the protein-coding genes (PCGs) and, comparatively, A and T contents were used more proportionally than C and G contents in all chosen mitogenomes. Chi-square analysis revealed the presence of putative optimal codons in all species, except in S. enflata. The correspondence analysis identified that mutational pressure and selection act on the mitogenomes of the selected chaetognaths and other phyla with varying intensities. The cluster analysis based on relative synonymous codon usage (RSCU) values revealed that RSCU variations in the PCGs of mitogenomes of chaetognaths are more comparable with those of protostomes. Apart from mutational pressure and selection, certain unknown selective forces might be acting on the PCGs in the analyzed mitogenomes as the phenomenon of SCUB could not be explained by mutational pressure, by selection, or by both.

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Mutational Pressure Drives Evolution of Synonymous Codon Usage in Genetically Distinct Oenothera plastomes

Cited by 6 publications

References 53 publications

From SARS and MERS CoVs to SARS‐CoV‐2: Moving toward more biased codon usage in viral structural and nonstructural genes

From SARS and MERS CoVs to SARS‐CoV‐2: Moving toward more biased codon usage in viral structural and nonstructural genes

Codon usage and codon pair patterns in non-grass monocot genomes

Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha

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