scholarly journals Codon Usage Bias Prefers AT Bases in Coding Sequences Among the Essential Genes of Haemophilus influenzae

2014 ◽  
Vol 6 (4) ◽  
pp. 417-421 ◽  
Author(s):  
Chakraborty SUPRIYO ◽  
Paul PROSENJIT ◽  
Tarikul Huda MAZUMDER
Keyword(s):  
Gene Expression ◽  
Haemophilus Influenzae ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Compositional Analysis ◽  
Revealed Preference ◽  
Nucleotide Composition ◽  
Essential Genes ◽  
Coding Sequences ◽  
Codon Positions

The base composition at three different codon positions in relation to codon usagebias and gene expressivity was studied in a sample of twenty five essential genes from Haemophilus influenzae. ENC, CBI and Fop were used to quantify the variation in codon usage bias for the cds. CAI is used to estimate the level of gene expression of the cds selected in the present study. To find out the relationship between the extent of codon bias and nucleotide composition the values of A, T, G, C and GC they were compared with the A3, T3, G3, C3 and GC3 values, respectively. The results showed relatively weak codon usage bias among the coding sequences (cds) of Haemophilus influenzae. This in turn, implies that the essential genes prefer to use a set of restricted codons. However, the base compositional analysis of essential genes in Haemophilus influenzae revealed preference of AT to GC bases within their coding sequences and this preference might affect gene expression as indicated by the relatively high CAI values ofthe coding sequences.

scholarly journals Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1087 ◽  
Author(s):  
Sheng-Lin Shi ◽  
Run-Xi Xia
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Nucleotide Composition ◽  
Effective Number ◽  
Bias Analysis ◽  
The Family ◽  
Usage Patterns ◽  
Codon Positions ◽  
Effective Number Of Codons

All iflavirus members belong to the unique genus, Iflavirus, of the family, Iflaviridae. The host taxa and sequence identities of these viruses are diverse. A codon usage bias, maintained by a balance between selection, mutation, and genetic drift, exists in a wide variety of organisms. We characterized the codon usage patterns of 44 iflavirus genomes that were isolated from the classes, Insecta, Arachnida, Mammalia, and Malacostraca. Iflaviruses lack a strong codon usage bias when they are evaluated using an effective number of codons. The odds ratios of the majority of dinucleotides are within the normal range. However, the dinucleotides at the 1st–2nd codon positions are more biased than those at the 2nd–3rd codon positions. Plots of effective numbers of codons, relative neutrality analysis, and PR2 bias analysis all indicate that selection pressure dominates mutations in shaping codon usage patterns in the family, Iflaviridae. When these viruses were grouped into their host taxa, we found that the indices, including the nucleotide composition, effective number of codons, relative synonymous codon usage, and the influencing factors behind the codon usage patterns, all show that there are non-significant differences between the six host-taxa-groups. Our results disagree with our assumption that diverse viruses should possess diverse codon usage patterns, suggesting that the nucleotide composition and codon usage in the family, Iflaviridae, are not host taxa-specific signatures.

Gene expression, nucleotide composition and codon usage bias of genes associated with human Y chromosome

Genetica ◽  
2017 ◽  
Vol 145 (3) ◽  
pp. 295-305 ◽  
Author(s):  
Monisha Nath Choudhury ◽  
Arif Uddin ◽  
Supriyo Chakraborty
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Y Chromosome ◽  
Codon Usage Bias ◽  
Nucleotide Composition ◽  
Human Y Chromosome

scholarly journals Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages

2021 ◽  
Vol 11 ◽  
Author(s):  
Yicong Li ◽  
Rui Wang ◽  
Huihui Wang ◽  
Feiyang Pu ◽  
Xili Feng ◽  
...  
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Essential Gene ◽  
Synonymous Codon ◽  
Phylogenetic Analyses ◽  
Nucleotide Composition ◽  
Synonymous Codon Usage ◽  
Related Gene ◽  
Codon Positions

Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 (atg13) is one essential gene for autophagy initiation, yet the evolutionary trends of the atg13 gene at the usages of nucleotide and synonymous codon remains unexplored. According to phylogenetic analyses for the atg13 gene of 226 eukaryotic organisms at the nucleotide and amino acid levels, it is clear that their nucleotide usages exhibit more genetic information than their amino acid usages. Specifically, the overall nucleotide usage bias quantified by information entropy reflected that the usage biases at the first and second codon positions were stronger than those at the third position of the atg13 genes. Furthermore, the bias level of nucleotide ‘G’ usage is highest, while that of nucleotide ‘C’ usage is lowest in the atg13 genes. On top of that, genetic features represented by synonymous codon usage exhibits a species-specific pattern on the evolution of the atg13 genes to some extent. Interestingly, the codon usages of atg13 genes in the ancestor animals (Latimeria chalumnae, Petromyzon marinus, and Rhinatrema bivittatum) are strongly influenced by mutation pressure from nucleotide composition constraint. However, the distributions of nucleotide composition at different codon positions in the atg13 gene display that natural selection still dominates atg13 codon usages during organisms’ evolution.

Comparative analysis of codon usage patterns in SARS-CoV-2, its mutants and other respiratory viruses

2021 ◽  
Author(s):  
Neetu Tyagi ◽  
Rahila Sardar ◽  
Dinesh Gupta
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Gc Content ◽  
Respiratory Illness ◽  
Respiratory Viruses ◽  
Nucleotide Composition ◽  
Health Crisis ◽  
Study Results ◽  
Usage Patterns ◽  
The Difference

AbstractThe Coronavirus disease 2019 (COVID-19) outbreak caused by Severe Acute Respiratory Syndrome Coronavirus 2 virus (SARS-CoV-2) poses a worldwide human health crisis, causing respiratory illness with a high mortality rate. To investigate the factors governing codon usage bias in all the respiratory viruses, including SARS-CoV-2 isolates from different geographical locations (~62K), including two recently emerging strains from the United Kingdom (UK), i.e., VUI202012/01 and South Africa (SA), i.e., 501.Y.V2 codon usage bias (CUBs) analysis was performed. The analysis includes RSCU analysis, GC content calculation, ENC analysis, dinucleotide frequency and neutrality plot analysis. We were motivated to conduct the study to fulfil two primary aims: first, to identify the difference in codon usage bias amongst all SARS-CoV-2 genomes and, secondly, to compare their CUBs properties with other respiratory viruses. A biased nucleotide composition was found as most of the highly preferred codons were A/U-ending in all the respiratory viruses studied here. Compared with the human host, the RSCU analysis led to the identification of 11 over-represented codons and 9 under-represented codons in SARS-CoV-2 genomes. Correlation analysis of ENC and GC3s revealed that mutational pressure is the leading force determining the CUBs. The present study results yield a better understanding of codon usage preferences for SARS-CoV-2 genomes and discover the possible evolutionary determinants responsible for the biases found among the respiratory viruses, thus unveils a unique feature of the SARS-CoV-2 evolution and adaptation. To the best of our knowledge, this is the first attempt at comparative CUBs analysis on the worldwide genomes of SARS-CoV-2, including novel emerged strains and other respiratory viruses.

scholarly journals Codon usage bias creates a ramp of hydrogen bonding at the 5′-end in prokaryotic ORFeomes

2019 ◽  
Author(s):  
Juan C. Villada ◽  
Maria F. Duran ◽  
Patrick K. H. Lee
Keyword(s):  
Hydrogen Bonding ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Translation Efficiency ◽  
Molecular Processes ◽  
Molecular Feature ◽  
Web Based ◽  
Synonymous Codons ◽  
Double Stranded Dna ◽  
Codon Positions

Codon usage bias exerts control over a wide variety of molecular processes. The positioning of synonymous codons within coding sequences (CDSs) dictates protein expression by mechanisms such as local translation efficiency, mRNA Gibbs free energy, and protein co-translational folding. In this work, we explore how codon variants affect the position-dependent content of hydrogen bonding, which in turn influences energy requirements for unwinding double-stranded DNA. By analyzing over 14,000 bacterial, archaeal, and fungal ORFeomes, we found that Bacteria and Archaea exhibit an exponential ramp of hydrogen bonding at the 5′-end of CDSs, while a similar ramp was not found in Fungi. The ramp develops within the first 20 codon positions in prokaryotes, eventually reaching a steady carrying capacity of hydrogen bonding that does not differ from Fungi. Selection against uniformity tests proved that selection acts against synonymous codons with high content of hydrogen bonding at the 5′-end of prokaryotic ORFeomes. Overall, this study provides novel insights into the molecular feature of hydrogen bonding that is governed by the genetic code at the 5′-end of CDSs. A web-based application to analyze the position-dependent hydrogen bonding of ORFeomes has been developed and is publicly available (https://juanvillada.shinyapps.io/hbonds/).

scholarly journals Genome-wide codon usage pattern analysis reveals the correlation between codon usage bias and gene expression in Cuscuta australis

Genomics ◽  
2020 ◽  
Vol 112 (4) ◽  
pp. 2695-2702 ◽  
Author(s):  
Xu-Yuan Liu ◽  
Yu Li ◽  
Kai-Kai Ji ◽  
Jie Zhu ◽  
Peng Ling ◽  
...  
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Pattern Analysis ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Genome Wide

scholarly journals COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences

2019 ◽  
Vol 11 (12) ◽  
pp. 3523-3528 ◽  
Author(s):  
Jérôme Bourret ◽  
Samuel Alizon ◽  
Ignacio G Bravo
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Null Hypothesis ◽  
Similarity Index ◽  
Bimodal Distribution ◽  
Added Value ◽  
Complete Analysis ◽  
Coding Sequences ◽  
Synonymous Codons ◽  
User Friendly

Abstract Codon Usage Preferences (CUPrefs) describe the unequal usage of synonymous codons at the gene, chromosome, or genome levels. Numerous indices have been developed to evaluate CUPrefs, either in absolute terms or with respect to a reference. We introduce the normalized index COUSIN (for COdon Usage Similarity INdex), that compares the CUPrefs of a query against those of a reference and normalizes the output over a Null Hypothesis of random codon usage. The added value of COUSIN is to be easily interpreted, both quantitatively and qualitatively. An eponymous software written in Python3 is available for local or online use (http://cousin.ird.fr). This software allows for an easy and complete analysis of CUPrefs via COUSIN, includes seven other indices, and provides additional features such as statistical analyses, clustering, and CUPrefs optimization for gene expression. We illustrate the flexibility of COUSIN and highlight its advantages by analyzing the complete coding sequences of eight divergent genomes. Strikingly, COUSIN captures a bimodal distribution in the CUPrefs of human and chicken genes hitherto unreported with such precision. COUSIN opens new perspectives to uncover CUPrefs specificities in genomes in a practical, informative, and user-friendly way.

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