Phylogenetic and Codon Usage Analysis for Capsid and Replicase Genes of Porcine Circovirus 3

Abstract Porcine circovirus type 3 (PCV3) is a highly contagious virus belonging to the family Circoviridae that causes the severe dermatitis and nephropathy syndrome. To date, PCV3 has a worldwide distribution and bring huge economic loss in swine industry. Replicase protein (Rep) and capsid protein (Cap) are two major proteins of PCV3. Considering that the large number of new PCV3 isolates were reported in the past few years and the research for the codon usage pattern of Rep and Cap genes was still a gap, phylogenetic and codon usage analysis of these two genes was performed. Phylogenetic analysis with all strains showed no clear clusters were displayed, but almost all strains of one genotype were separated into same clade. Relative synonymous codon usage (RSCU) analysis revealed that the codon usage bias existed and effective number of codon (ENC) analysis showed that the bias was slight low. ENC-GC3s plot indicated that mutational pressure and other factors both play a role in PCV3 codon usage and neutrality plot analysis showed that natural selection was the main force influencing the codon usage pattern. In summary, the results provided the important basic data on codon usage pattern of Rep and Cap genes, and a better understanding of the evolution and potential origin of PCV3.

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Analysis of codon usage bias of classical swine fever virus

Veterinary World ◽

10.14202/vetworld.2021.1450-1458 ◽

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.

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The characteristics of the synonymous codon usage in hepatitis B virus and the effects of host on the virus in codon usage pattern

Virology Journal ◽

10.1186/1743-422x-8-544 ◽

2011 ◽

Vol 8 (1) ◽

Cited By ~ 13

Author(s):

Ming-ren Ma ◽

Xiao-qin Ha ◽

Hui Ling ◽

Mei-liang Wang ◽

Fang-xin Zhang ◽

...

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Codon Usage ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Codon Usage Pattern ◽

Usage Pattern ◽

B Virus

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P1063 THE CHARACTERISTICS OF THE SYNONYMOUS CODON USAGE PATTERN OF rtN236T MUTATION IN CHRONIC HEPATITIS B PATIENTS TREATED WITH ADEFOVIR DIPIVOXIL: PYROSEQUENCING ANALYSIS OF 1418 CASES

Journal of Hepatology ◽

10.1016/s0168-8278(14)61223-x ◽

2014 ◽

Vol 60 (1) ◽

pp. S431

Author(s):

W. Hou ◽

W. Lu

Keyword(s):

Chronic Hepatitis ◽

Hepatitis B ◽

Codon Usage ◽

Chronic Hepatitis B ◽

Adefovir Dipivoxil ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Codon Usage Pattern ◽

Usage Pattern ◽

Pyrosequencing Analysis

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Synonymous codon usage pattern analysis of Hepatitis D virus

Virus Research ◽

10.1016/j.virusres.2013.01.007 ◽

2013 ◽

Vol 173 (2) ◽

pp. 350-353 ◽

Cited By ~ 5

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

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

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.204-210.649 ◽

2011 ◽

Vol 204-210 ◽

pp. 649-662 ◽

Cited By ~ 1

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.

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