Analysis of synonymous codon usage in the VP2 protein gene of infectious bursal disease virus

Kumar, Chandra Shekhar; Hazarika, Nazia M. J.; Kumar, Sachin

doi:10.1007/s00705-015-2505-0

Cited by 8 publications

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References 36 publications

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“…Factors like natural selection, mutational pressure, translational efficiency, and compositional constraints mostly influence the synonymous codon usage bias within an organism . Codon usage bias has been explored in order to understand the evolutionary biology of different viruses . In NDV variation of synonymous codon usage pattern is gene function and geography specific but not host specific .…”

Section: Introductionmentioning

confidence: 99%

Synonymous codon usage of genes in polymerase complex of Newcastle disease virus

Kumar

2017

J Basic Microbiol

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Newcastle disease virus (NDV) is pathogenic to both avian and non-avian species but extensively finds poultry as its primary host and causes heavy economic losses in the poultry industry. In this study, a total of 186 polymerase complex comprising of nucleoprotein (N), phosphoprotein (P), and large polymerase (L) genes of NDV was analyzed for synonymous codon usage. The relative synonymous codon usage and effective number of codons (ENC) values were used to estimate codon usage variation in each gene. Correspondence analysis (COA) was used to study the major trend in codon usage variation. Analyzing the ENC plot values against GC3s (at synonymous third codon position) we concluded that mutational pressure was the main factor determining codon usage bias than translational selection in NDV N, P, and L genes. Moreover, correlation analysis indicated, that aromaticity of N, P, and L genes also influenced the codon usage variation. The varied distribution of pathotypes for N, P, and L gene clearly suggests that change in codon usage for NDV is pathotype specific. The codon usage preference similarity in N, P, and L gene might be detrimental for polymerase complex functioning. The study represents a comprehensive analysis to date of N, P, and L genes codon usage pattern of NDV and provides a basic understanding of the mechanisms for codon usage bias.

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Section: Introductionmentioning

confidence: 99%

Synonymous codon usage of genes in polymerase complex of Newcastle disease virus

Kumar

2017

J Basic Microbiol

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Exploring Codon Usage Patterns and Influencing Factors in Ranavirus DNA Polymerase Genes

Aktürk Dizman

2024

Journal of Basic Microbiology

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Ranaviruses, members of the genus Ranavirus within the family Iridoviridae, have become a significant concern for amphibian populations globally, along with other cold‐blooded vertebrates, due to their emergence as a significant threat. We employed bioinformatics tools to examine the codon usage patterns in 61 DNA pol genes from Ranavirus, Lymphocystivirus, Megalocytivirus, and two unclassified ranaviruses, as no prior studies had been conducted on this topic. The results showed a slight or low level of codon usage bias (CUB) in the DNA pol genes of Ranavirus. Relative synonymous codon usage (RSCU) analysis indicated that the predominant codons favored in Ranavirus DNA pol genes terminate with C or G. Correlation analysis examining nucleotide content, third codon position, effective number of codons (ENC), correspondence analysis (COA), Aroma values, and GRAVY values indicated that the CUB across DNA pol genes could be influenced by both mutation pressure and natural selection. The neutrality plot indicated that natural selection is the primary factor driving codon usage. Furthermore, the analysis of the codon adaptation index (CAI) illustrated the robust adaptability of Ranavirus DNA pol genes to their hosts. Analysis of the relative codon deoptimization index (RCDI) suggested that Ranavirus DNA pol genes underwent greater selection pressure from their hosts. These findings will aid in comprehending the factors influencing the evolution and adaptation of Ranavirus to its hosts.

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Synonymous codon usage pattern in glycoprotein gene of rabies virus

Morla

Makhija

Kumar

2016

Gene

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Analysis of synonymous codon usage in the VP2 protein gene of infectious bursal disease virus

Cited by 8 publications

References 36 publications

Synonymous codon usage of genes in polymerase complex of Newcastle disease virus

Synonymous codon usage of genes in polymerase complex of Newcastle disease virus

Exploring Codon Usage Patterns and Influencing Factors in Ranavirus DNA Polymerase Genes

Synonymous codon usage pattern in glycoprotein gene of rabies virus

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