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 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.

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 Synonymous codon usage pattern among the S, M, and L segments in crimean-congo hemorrhagic fever causing virus

2021 ◽  
Vol 17 (4) ◽  
pp. 479-491
Author(s):  
Mallikarjun S Beelagi ◽  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Hemorrhagic Fever ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Depth Information ◽  
Usage Pattern ◽  
Crimean Congo Hemorrhagic Fever ◽  
Cchf Virus

Crimean-congo hemorrhagic fever (CCHF) virus is one among the major zoonosis viral diseases that use the Hyalomma ticks as their transmission vector to cause viral infection to the human and mammalian community. The fatality of infectious is high across the world especially in Africa, Asia, Middle East, and Europe. This study regarding codon usage bias of S, M, and L segments of the CCHF virus pertaining to the host Homo sapiens, reveals in-depth information about the evolutionary characteristics of CCHFV. Relative Synonymous Codon Usage (RSCU), Effective number of codons (ENC) were calculated, to determine the codon usage pattern in each segment. Correlation analysis between Codon adaptation index (CAI), GRAVY (Hydrophobicity), AROMO (Aromaticity), and nucleotide composition revealed bias in the codon usage pattern. There was no strong codon bias found among any segments of the CCHF virus, indicating both the factors i.e., natural selection and mutational pressure shapes the codon usage bias.

Characterization of Synonymous Codon Usage Bias in the Riemerella Anatipestifer Major Facilitator Superfamily Mfs_1 Gene Encoded 492 Amino Acids Protein

2013 ◽  
Vol 641-642 ◽  
pp. 675-683
Author(s):  
Xin Zhang ◽  
An Chun Cheng ◽  
Ming Shu Wang ◽  
De Kang Zhu ◽  
Xiao Jia Wang ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Position ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Major Facilitator Superfamily ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Major Facilitator ◽  
Synonymous Codon Usage Bias

Objective: The aim was to identify the codon usage bias between the newly identified Riemerella anatipestifer (RA) major facilitator superfamily mfs_1 gene (GenBank accession No.CP003388.1) and other reference bacteriums. Methods: A comparative analysis of the codon usage bias of the 18 bacteriums was performed by using the CodonW 1.4 program and CUSP (create a codon usage table) program of EMBOSS (The European Molecular Biology Open Software Suite). Results: The results showed obvious differences of the synonymous codon usage bias in the 18 bacteriums indicated by the Codon Adaptation Index (CAI), effective number of codons (ENc), and the value of G+C content at the 3rd codon position. The codon usage pattern of the major facilitator superfamily mfs_1 gene was phylogenetically conserved and similar to that of the major facilitator superfamily mfs_1 gene of the Elizabethkingia anophelis Ag1 Contig17, with a strong bias towards the codons with A and T at the 3rd codon position. A cluster analysis of codon usage pattern of the RA major facilitator superfamily mfs_1 gene with other reference bacteriums demonstrated that the codon usage bias of the major facilitator superfamily mfs_1 genes of the 18 bacteriums had a very close relation with their gene function. The ENc-plot revealed that the genetic heterogeneity in the RA major facilitator superfamily mfs_1 gene and the 18 reference bacteriums were constrained by G+C content, while gene length exerted relatively weaker influences. In addition, comparisons of the codon preferences in the major facilitator superfamily mfs_1 gene of RA with those of Escherichia coli, yeast and humans revealed that there were 36 codons showing distinct usage differences between the RA and E. coli, and 37 between the RA and humans, but only 28 between the RA and yeast. Therefore, the yeast system may be more suitable for the expression of the RA major facilitator superfamily mfs_1 gene. Conclusion: Together, these results may improve our understanding of the evolution, pathogenesis and functional studies of RA and possibly contribute significantly to the area of other bacteriums.

Analysis of synonymous codon usage inShigella flexneri2a strain 301 and otherShigellaandEscherichia colistrains

2011 ◽  
Vol 57 (12) ◽  
pp. 1016-1023 ◽  
Author(s):  
Xue Lian Luo ◽  
Jian Guo Xu ◽  
Chang Yun Ye
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Shigella Flexneri ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Mutational Pressure ◽  
E Coli ◽  
Shigella Flexneri 2A ◽  
Usage Patterns

In this study, we analysed synonymous codon usage in Shigella flexneri 2a strain 301 (Sf301) and performed a comparative analysis of synonymous codon usage patterns in Sf301 and other strains of Shigella and Escherichia coli . Although there was a significant variety in codon usage bias among different Sf301 genes, there was a slight but observable codon usage bias that could primarily be attributable to mutational pressure and translational selection. In addition, the relative abundance of dinucleotides in Sf301 was observed to be independent of the overall base composition but was still caused by differential mutational pressure; this also shaped codon usage. By comparing the relative synonymous codon usage values across different Shigella and E. coli strains, we suggested that the synonymous codon usage pattern in the Shigella genomes was strain specific. This study represents a comprehensive analysis of Shigella codon usage patterns and provides a basic understanding of the mechanisms underlying codon usage bias.

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

Synonymous codon usage pattern analysis of Hepatitis D virus

2013 ◽  
Vol 173 (2) ◽  
pp. 350-353 ◽  
Author(s):  
Arghya Kamal Bishal ◽  
Rashmi Mukherjee ◽  
Chandan Chakraborty
Keyword(s):  
Codon Usage ◽  
Pattern Analysis ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Usage Pattern ◽  
Hepatitis D ◽  
Hepatitis D Virus

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.

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