scholarly journals Comprehensive Analysis and Comparison on the Codon Usage Pattern of Whole Mycobacterium tuberculosis Coding Genome from Different Area

2018 ◽  
Vol 2018 ◽  
pp. 1-7 ◽  
Author(s):  
Li Gun ◽  
Ren Yumiao ◽  
Pan Haixian ◽  
Zhang Liang
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Gc Content ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Strong Negative Correlation ◽  
Synonymous Codons ◽  
The Relationship ◽  
Adaptation Index

Phenomenon of unequal use of synonymous codons in Mycobacterium tuberculosis is common. Codon usage bias not only plays an important regulatory role at the level of gene expression, but also helps in improving the accuracy and efficiency of translation. Meanwhile, codon usage pattern of Mycobacterium tuberculosis genome is important for interpreting evolutionary characteristics in species. In order to investigate the codon usage pattern of the Mycobacterium tuberculosis genome, 12 Mycobacterium tuberculosis genomes from different area are downloaded from the GeneBank. The correlations between G3, GC12, whole GC content, codon adaptation index, codon bias index, and so on of Mycobacterium tuberculosis genomes are calculated. The ENC-plot, relationship between A3/(A3+T3) and G3/(G3+C3), GC12 versus GC3 plot, and the RSCU of overall/separated genomes all show that the codon usage bias exists in all 12 Mycobacterium tuberculosis genomes. Lastly, relationship between CBI and the equalization of ENC shows a strong negative correlation between them. The relationship between protein length and GC content (GC3 and GC12) shows that more obvious differences in the GC content may be in shorter protein. These results show that codon usage bias existing in the Mycobacterium tuberculosis genomes could be used for further study on their evolutionary phenomenon.

scholarly journals Analysis of Synonymous Codon Usage Bias in Flaviviridae Virus

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Huipeng Yao ◽  
Mengyu Chen ◽  
Zizhong Tang
Keyword(s):  
Phylogenetic Analysis ◽  
Natural Selection ◽  
Correlation Analysis ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Yellow Fever Virus ◽  
Gc Content ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Group I

Background. Flaviviridae viruses are single-stranded, positive-sense RNA viruses, which threat human constantly mediated by mosquitoes, ticks, and sandflies. Considering the recent increase in the prevalence of the family virus and its risk potential, we investigated the codon usage pattern to understand its evolutionary processes and provide some useful data to develop the medications for most of Flaviviridae viruses. Results. The overall extent of codon usage bias in 65 Flaviviridae viruses is low with the average value of GC contents being 50.5% and the highest value being 55.9%; the lowest value is 40.2%. ENC values of Flaviviridae virus genes vary from 48.75 to 57.83 with a mean value of 55.56. U- and A-ended codons are preferred in the Flaviviridae virus. Correlation analysis shows that the positive correlation between ENC value and GC content at the third nucleotide positions was significant in this family virus. The result of analysis of ENC, neutrality plot analysis, and correlation analysis revealed that codon usage bias of all the viruses was affected mainly by natural selection. Meanwhile, according to correspondence analysis (CoA) based on RSCU and phylogenetic analysis, the Flaviviridae viruses mainly are made up of two groups, Group I (Yellow fever virus, Apoi virus, Tembusu virus, Dengue virus 1, and others) and Group II (West Nile virus lineage 2, Japanese encephalitis virus, Usutu virus, Kedougou virus, and others). Conclusions. All in, the bias of codon usage pattern is affected not only by compositional constraints but also by natural selection. Phylogenetic analysis also illustrates that codon usage bias of virus can serve as an effective means of evolutionary classification in Flaviviridae virus.

scholarly journals Analysis of codon usage bias of classical swine fever virus

2021 ◽  
pp. 1450-1458
Author(s):  
Sharanagouda S. Patil ◽  
Uma Bharathi Indrabalan ◽  
Kuralayanapalya Puttahonnappa Suresh ◽  
Bibek Ranjan Shome
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Principal Component ◽  
Infectious Agent ◽  
Classical Swine Fever ◽  
Economic Loss ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Coding Regions

Background and Aim: Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease in pigs causing 100% mortality in susceptible adult pigs and piglets. High mortality rate in pigs causes huge economic loss to pig farmers. CSFV has a positive-sense RNA genome of 12.3 kb in length flanked by untranslated regions at 5' and 3' end. The genome codes for a large polyprotein of 3900 amino acids coding for 11 viral proteins. The 1300 codons in the polyprotein are coded by different combinations of three nucleotides which help the infectious agent to evolve itself and adapt to the host environment. This study performed and employed various methods/techniques to estimate the changes occurring in the process of CSFV evolution by analyzing the codon usage pattern. Materials and Methods: The evolution of viruses is widely studied by analyzing their nucleotides and coding regions/ codons using various methods. A total of 115 complete coding regions of CSFVs including one complete genome from our laboratory (MH734359) were included in this study and analysis was carried out using various methods in estimating codon usage bias and evolution. This study elaborates on the factors that influence the codon usage pattern. Results: The effective number of codons (ENC) and relative synonymous codon usage showed the presence of codon usage bias. The mononucleotide (A) has a higher frequency compared to the other mononucleotides (G, C, and T). The dinucleotides CG and CC are underrepresented and overrepresented. The codons CGT was underrepresented and AGG was overrepresented. The codon adaptation index value of 0.71 was obtained indicating that there is a similarity in the codon usage bias. The principal component analysis, ENC-plot, Neutrality plot, and Parity Rule 2 plot produced in this article indicate that the CSFV is influenced by the codon usage bias. The mutational pressure and natural selection are the important factors that influence the codon usage bias. Conclusion: The study provides useful information on the codon usage analysis of CSFV and may be utilized to understand the host adaptation to virus environment and its evolution. Further, such findings help in new gene discovery, design of primers/probes, design of transgenes, determination of the origin of species, prediction of gene expression level, and gene function of CSFV. To the best of our knowledge, this is the first study on codon usage bias involving such a large number of complete CSFVs including one sequence of CSFV from India.

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 Comparative studies of codon usage profile of Anisakis simplex (Nematoda) and Carassius gibelio (Prussian carp)

2022 ◽  
Vol 43 (1) ◽  
pp. 123-132
Author(s):  
W. Ahmed ◽  
◽  
S. Gupta ◽  
I. Mukherjee ◽  
V.K. Babu ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Similar Pattern ◽  
Synonymous Codon ◽  
Anisakis Simplex ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Prussian Carp ◽  
Evolutionary Forces ◽  
Carassius Gibelio

Aim: The aim of the present study was to understand the molecular relationship between nematode (parasite) and fish (host) through codon usage bias (CUB) analysis. Methodology: The Codon usage bias analysis has been performed in fish Carassius gibelio (Prussian carp) and nematode fish parasite Anisakis simplex. The complete coding sequences (CDS) of C. gibelio (Prussian carp) and A. simplex (Nematode) were retrieved from National Center for Biotechnology Information and followed to that we have performed bioinformatics analysis to understand the codon usage pattern between host and parasite. Results: Different CUB indices like Relative synonymous codon usage (RSCU), Effective number of codons (ENC), Codon adaptation index (CAI) and Codon bias index (CBI) revealed a similar pattern in the codon usage in C. gibelio and A. simplex. In addition, inclusive analysis using different plots (ENC, parity, neutrality) had shown the influence of both the evolutionary forces i.e mutational and translational selection on codon usage pattern. This describes the role of evolutionary forces in determining the conserved genome to establish species-specific function-level differences for efficient survival. Interpretation: The present study elucidated the association between Carassiusgibelio (host) and Anisakis simplex (parasite) based on the similar pattern of codon usage bias between both the species.

scholarly journals Characterization of codon usage pattern in novel coronavirus 2019-nCoV

2020 ◽  
Author(s):  
Wei Hou
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
International Health ◽  
Bioinformatic Analysis ◽  
Viral Pneumonia ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Potential Value ◽  
Novel Coronavirus

Abstract The outbreak of viral pneumonia in China due to a novel coronavirus 2019-nCoV poses significant threats to international health. In this study we perform bioinformatic analysis to take a snapshot of the codon usage pattern of 2019-nCoV and uncover that this novel coronavirus has a relatively low codon usage bias. The information from this research may not only be helpful to get new insights into the evolution of 2019-nCoV, but also have potential value for developing coronavirus vaccines.

Characterization of Codon Usage Bias in the UL55 Gene of Duck Enteritis Virus

2011 ◽  
Vol 204-210 ◽  
pp. 649-662 ◽  
Author(s):  
Ying Wu ◽  
An Chun Cheng ◽  
Ming Shu Wang ◽  
De Kang Zhu ◽  
Xiao Yue Chen
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Duck Enteritis Virus ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
E Coli ◽  
Usage Patterns ◽  
Enteritis Virus

The analysis of codon usage may improve our understanding of the evolution and pathogenesis of DEV（Duck enteritis virus） and allow reengineering of target gene to improve their expression for gene therapy.In this study,we calculated the codon usage bias in DEV UL55 gene and performed a comparative analysis of synonymous codon usage patterns in other 26 related viruses by EMBOSS CUSP program and Codon W on line.Moreover,statistical methods were used to investigate the correlations of these related parameters. By comparing synonymous codon usage patterns in different viruses,we observed that synonymous codon usage pattern in these virus is virus specific and phylogenetically conserved, with a strong bias towards the codons with A and T at the third codon position. Phylogenetic analysis based on codon usage pattern suggested that DEV UL55 gene was clustered with the avian Alphaherpesvirus but diverged to form a single branch. The Neutrality-plot suggested GC12 and GC3s adopt the same mutation pattern,meanwhile,the ENC-plot revealed that the genetic heterogeneity in UL55 genes is constrained by the G+C content, while translational selection and gene length have no or micro effect on the variations of synonymous codon usage in these virus genes.Furthermore, we compared the codon preferences of DEV with those of E. coli, yeast and Homo sapiens.Data suggested the eukaryotes system such as human system may be more suitable for the expression of DEV UL55 gene in vitro. If the yeast and E. coli expression system are wanted for the expression of DEV UL55 gene ,codon optimization of the DEV UL55 gene may be required.

scholarly journals Comparisons of Coding and Noncoding Sequences to infer the Origin of Codon usage Bias

2017 ◽  
Author(s):  
Prashant Mainali ◽  
Sobita Pathak
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Gc Content ◽  
Mutation Bias ◽  
Translation Process ◽  
Noncoding Regions ◽  
Coding Regions ◽  
Synonymous Codons ◽  
Shed Light

ABSTRACTCodon usage bias is the preferential use of the subset of synonymous codons during translation. In this paper, the comparisons of normalized entropy and GC content between the sequence of coding regions of Escherichia coli k12 and noncoding regions (ncRNA, rRNA) of various organisms were done to shed light on the origin of the codon usage bias.The normalized entropy of the coding regions was found significantly higher than the noncoding regions, suggesting the role of the translation process in shaping codon usage bias. Further, when the position specific GC content of both coding and noncoding regions was analyzed, the GC2 content in coding regions was lower than GC1 and GC2 while in noncoding regions, the GC1, GC2, GC3 contents were approximately equal. This discrepancy is explained by the biased mutation coupled with the presence and absence of selection pressure. The accumulation of CG content occurs in the sequences due to mutation bias in DNA repair and recombination process. In noncoding regions, the mutation is harmful and thus, selected against while due to the degeneracy of codons in coding regions, a mutation in GC3 is neutral and hence, not selected. Thus, the accumulation of GC content occurs in coding regions, and thus codon usage bias occurs.

Analysis of Codon Usage in Herpesvirus Glycoprotein B (gB) Gene

2011 ◽  
Vol 343-344 ◽  
pp. 721-728
Author(s):  
Long Jiang ◽  
An Chun Cheng ◽  
Ming Shu Wang ◽  
De Kang Zhu ◽  
Ren Yong Jia
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Position ◽  
Pearson Correlation ◽  
Gc Content ◽  
Correlation Coefficients ◽  
Mutational Bias ◽  
Synonymous Codons ◽  
Base Position ◽  
Two Factors

Due to the degeneracy of genetic code, most amino acids are coded by more than one codon (synonymous codons). The synonymous codons are not used at equal frequencies both within and between organisms. Of the total 33 herpesvirus gB genes, approximately 9.1% of the total gB genes had low codon bias (ENC<35), 72.7% of the gB genes had high ENC values (ENC>50), indicating that these gB genes had random codon usage in herpesviruses. There might be no direct correlation between the codon usage bias and the host, which indicates that the tRNA abundance of the host was not the main factor influencing the codon usage bias. A plot of ENC vs. GC3 indicates that mutational bias may be a more important factor than tRNA abundance in determining codon usage bias of herpesvirus gB genes. Pearson correlation coefficients between the ENC value and corresponding GC%, cumulative GC% in 2nd (GC2%) and 3rd codon position (GC3%) of each herpesvirus gB gene were -0.621 (p<0.01), -0.656 (p<0.01) and -0.712 (p<0.01), respectively, which implies that significant correlations existed between them. But no significant correlations existed between ENC and cumulative GC% in 1st codon position of each herpesviral gB gene. Furthermore, significant correlations also existed between GC% and GC3% of 33 herpesvirus gB genes (r=0.856, p<0.01). So it seems that, GC content, and particularly GC content at the 3rd base position, contributing greatly to the effective number of codons, indicating that the mutational bias dominates over translational selection. Further analysis on the relationship between gene length and ENC of 33 herpesvirus gB genes demonstrated that the two factors were not correlated. Significant correlations were found between the gene expression levels assessed by CAI value and ENC (r = -0.424, p<0.05) and GC3 values (r = 0.644, p<0.01).

scholarly journals Patterns of Codon Usage Bias in WRKY Genes of Brassica rapa and Arabidopsis thaliana

2019 ◽  
Vol 11 (4) ◽  
pp. 76
Author(s):  
Snigdha Srivastava ◽  
Sheetal Chanyal ◽  
Ashutosh Dubey ◽  
A. K. Tewari ◽  
Gohar Taj
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factor ◽  
Codon Usage ◽  
Brassica Rapa ◽  
Stress Responses ◽  
Codon Usage Bias ◽  
Wrky Transcription Factor ◽  
Codon Usage Pattern ◽  
Transcription Factor Family ◽  
Synonymous Codons

Codon usage bias (CUB) is defined as the selective and nonrandom use of synonymous codons by the organism for encoding the amino acids. One of the important plant transcription factor family is the &lsquo;WRKY&rsquo; whose role has been investigated in the regulation of abiotic and biotic stress responses in plants. In this paper, the codon usage pattern of the WRKY transcription factor of the two important plant species Arabidopsis thaliana and Brassica rapa has been investigated. Various codon usage indices like ENc, CAI, correspondence analysis, RSCU analysis, neutrality plot and hierarchial clustering has been done. The GC codon status was high in Arabidopsis. The RSCU analysis of codons revealed that codons coding for arginine was maximum in both the plant species.Our results propose that natural selection was the main dominating factor guiding the evolution of different WRKY genes in both Arabidopsis thaliana and Brassica rapa.

scholarly journals The optimization of mRNA expression level by its intrinsic properties—insights from codon usage pattern and structural stability of mRNA

2017 ◽  
Author(s):  
Manish P Victor ◽  
Debarun Acharya ◽  
Tina Begum ◽  
Tapash C Ghosh
Keyword(s):  
Gene Expression ◽  
Codon Usage ◽  
Mrna Expression ◽  
Mrna Stability ◽  
Codon Usage Bias ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Mrna Expression Level ◽  
Wild Type ◽  
Codon Composition

AbstractThe deviation from the uniform usage of synonymous codons is termed codon usage bias. A lot has been explained from the translational viewpoint for the observed phenomenon. To understand codon usage bias from the transcriptional perspective, we present here a holistic picture of this phenomenon in Saccharomyces cerevisiae, using both wild type and computationally mutated mRNAs. Although in wild type, both codon usage bias and mRNA stability positively regulate the gene (mRNA) expression level and are positively correlated with each other, any deviation from natural situation breaks such equilibrium. Computational examination of mRNA sequences with different sets of synonymous codon composition reveals that in mutated condition, the mRNA expression becomes reduced. Furthermore, constraining codon usage pattern to wild type and carrying out randomization of codons resulted in less stable mRNA. Further, we realized a Boolean Expression explaining the gene expression under various conditions of bias and mRNA stability. These studies suggest that selection of codons is favored for regulation of gene expression through potential formation of messenger RNA structures which contribute to folding stability. The naturally occurring codon composition is responsible for optimization of gene expression, and under such composition, the mRNA structure having highest stability is selected by nature.

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