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

Beelagi, Mallikarjun S; Kumar, SR Santosh; Indrabalan, Uma Bharathi; Patil, S. S.; Prasad, Ashwini; SURESH, K P; Kollur, Shiva Prasad; Jayappa, Veeresh Santhebennur; Kakkalameli, Siddappa B; Srinivasa, Chandrashekar; Venkataravana, Prabhakarareddy Anapalli; Shivamallu, Chandan

doi:10.6026/97320630017479

Cited by 8 publications

(9 citation statements)

References 21 publications

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“…PXY > 1.23 is regarded as high relative abundance, whereas PXY < 0.78 is considered low relative abundance. The required external library "seqinR" was used to determine the dinucleotide frequencies in the R Studio programming language [8].…”

Section: Relative Dinucleotide Abundance Analysismentioning

confidence: 99%

“…Where g ij is the observed number of the i th codon for the j th amino acid, and ni is the number of synonymous codons. R Studio programming software (https://cran.r-project.org) and the "seqinR" library were used to obtain and visualize RSCU values for all seven Pestiviruses [8].…”

Section: Relative Synonymous Codon Usage (Rscu) Analysismentioning

confidence: 99%

“…The ENC plot was generated to show the relationship between the ENC and GC3 frequencies (the sum of G&C nucleotide at the third codon position). Furthermore, this precise method for estimating absolute synonymous codon usage, defines and quantifies codon usage bias in a gene or genome [8,21]. The formula for calculating ENC plot values is ( )…”

Section: The Effective Number Of Codons (Enc) Analysismentioning

confidence: 99%

“…Where s indicates the GC3 content. If the ENC values fall on the standard curve, it indicates that mutational pressure is the only factor influencing the codon usage and the values that fall below the standard curve show that the codon bias is constrained by another factor, that is, natural selection [8,21].…”

Section: The Effective Number Of Codons (Enc) Analysismentioning

confidence: 99%

“…In addition, the extent to which the bias in the codon usage pattern affects viral-host adaptiveness influences replication efficiency, virulence, protein synthesis, and virus survival. Several studies have suggested that mutational pressure is the primary driving force behind the formation of a codon use pattern [8,9].…”

Section: Introductionmentioning

confidence: 99%

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The first study on analysis of the codon usage bias and evolutionary analysis of the glycoprotein envelope E2 gene of seven Pestiviruses

et al. 2022

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Background and Aim: Pestivirus, a genus of the Flaviviridae family, comprises viruses that affect bovines, sheep, and pigs. Symptoms, including hemorrhagic syndromes, abortion, respiratory complications, and deadly mucosal diseases, are produced in infected animals, which cause huge economic losses to the farmers. Bovine viral diarrhea virus-1, bovine viral diarrhea virus-2, classical swine fever virus, border disease virus, Bungowannah, Hobi-like, and atypical porcine pestivirus belonging to the Pestivirus genus were selected for the study. This study aimed to estimate the codon usage bias and the rate of evolution using the glycoprotein E2 gene. Furthermore, codon usage bias analysis was performed using publicly available nucleotide sequences of the E2 gene of all seven Pestiviruses. These nucleotide sequences might elucidate the disease epidemiology and facilitate the development of designing better vaccines. Materials and Methods: Coding sequences of the E2 gene of Pestiviruses A (n = 89), B (n = 60), C (n = 75), D (n = 10), F (n = 07), H (n = 52), and K (n = 85) were included in this study. They were analyzed using different methods to estimate the codon usage bias and evolution. In addition, the maximum likelihood and Bayesian methodologies were employed to analyze a molecular dataset of seven Pestiviruses using a complete E2 gene region. Results: The combined analysis of codon usage bias and evolutionary rate analysis revealed that the Pestiviruses A, B, C, D, F, H, and K have a codon usage bias in which mutation and natural selection have played vital roles. Furthermore, while the effective number of codons values revealed a moderate bias, neutrality plots indicated the natural selection in A, B, F, and H Pestiviruses and mutational pressure in C, D, and K Pestiviruses. The correspondence analysis revealed that axis-1 significantly contributes to the synonymous codon usage pattern. In this study, the evolutionary rate of Pestiviruses B, H, and K was very high. The most recent common ancestors of all Pestivirus lineages are 1997, 1975, 1946, 1990, 2004, 1990, and 1990 for Pestiviruses A, B, C, D, F, H, and K, respectively. This study confirms that both mutational pressure and natural selection have played a significant role in codon usage bias and evolutionary studies. Conclusion: This study provides insight into the codon usage bias and evolutionary lineages of pestiviruses. It is arguably the first report of such kind. The information provided by the study can be further used to elucidate the respective host adaptation strategies of the viruses. In turn, this information helps study the epidemiology and control methods of pestiviruses.

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Section: Relative Dinucleotide Abundance Analysismentioning

confidence: 99%

Section: Relative Synonymous Codon Usage (Rscu) Analysismentioning

confidence: 99%

Section: The Effective Number Of Codons (Enc) Analysismentioning

confidence: 99%

Section: The Effective Number Of Codons (Enc) Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The first study on analysis of the codon usage bias and evolutionary analysis of the glycoprotein envelope E2 gene of seven Pestiviruses

et al. 2022

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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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Evaluation of codon usage patterns and molecular evolution dynamics in Japanese encephalitis virus: An integrated bioinformatics approach

Suresh

Indrabalan

Shreevatsa

et al. 2023

Infection, Genetics and Evolution

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

Cited by 8 publications

References 21 publications

The first study on analysis of the codon usage bias and evolutionary analysis of the glycoprotein envelope E2 gene of seven Pestiviruses

The first study on analysis of the codon usage bias and evolutionary analysis of the glycoprotein envelope E2 gene of seven Pestiviruses

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

Evaluation of codon usage patterns and molecular evolution dynamics in Japanese encephalitis virus: An integrated bioinformatics approach

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