scholarly journals Patterns of Synonymous Codon Usage on Human Metapneumovirus and Its Influencing Factors

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Qiao Zhong ◽  
Weidong Xu ◽  
Yuanjian Wu ◽  
Hongxing Xu
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Influence Factor ◽  
Synonymous Codon ◽  
Acute Respiratory Tract Infection ◽  
Synonymous Codon Usage ◽  
Human Metapneumovirus ◽  
Host Cells ◽  
Phylogenetic Distance ◽  
Mutation Pressure

Human metapneumovirus (HMPV) is an important agent of acute respiratory tract infection in children, while its pathogenicity and molecular evolution are lacking. Herein, we firstly report the synonymous codon usage patterns of HMPV genome. The relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents, and correlation analysis were performed among 17 available whole genome of HMPV, including different genotypes. All preferred codons in HMPV are ended with A/U nucleotide and exhibited a great association with its high proportion of these two nucleotides in their genomes. Mutation pressure rather than natural selection is the main influence factor that determines the bias of synonymous codon usage in HMPV. The complementary pattern of codon usage bias between HMPV and human cell was observed, and this phenomenon suggests that host cells might be also act as an important factor to affect the codon usage bias. Moreover, the codon usage biases in each HMPV genotypes are separated into different clades, which suggest that phylogenetic distance might involve in codon usage bias formation as well. These analyses of synonymous codon usage bias in HMPV provide more information for better understanding its evolution and pathogenicity.

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 Characteristics of synonymous codon usage bias in the beginning region of West Nile virus

2014 ◽  
Vol 13 (3) ◽  
pp. 7347-7355 ◽  
Author(s):  
X.X. Ma ◽  
Y.P. Feng ◽  
J.L. Liu ◽  
L. Chen ◽  
Y.Q. Zhao ◽  
...  
Keyword(s):  
West Nile Virus ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
West Nile ◽  
In The Beginning ◽  
Synonymous Codon Usage Bias

Host Adaptation of Codon Usage in SARS-CoV-2 From Mammals Indicate Natural Selection

2021 ◽  
Author(s):  
Yanan Fu ◽  
Yanping Huang ◽  
Jingjing Rao ◽  
Feng Zeng ◽  
Ruiping Yang ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Binding Affinity ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Host Adaptation ◽  
Synonymous Codon Usage ◽  
Mutation Pressure ◽  
Usage Analysis ◽  
Human Receptor

Abstract The outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, spread across hosts from humans to animals, transmitting particularly effectively in mink. How SARS-CoV-2 selects and evolves in the host, and the differences in the evolution of different animals are still unclear. To analysis the mutation and codon usage bias of SARS-CoV-2 in infected humans and animals. The SARS-CoV-2 sequence in mink (Mink-SARS2) and binding energy with receptor were calculated compared with human. The relative synonymous codon usage of viral encoded gene was analyzed to characterize the differences and the evolutionary characteristics. A synonymous codon usage analysis showed that SARS-CoV-2 is optimized to adapt in the animals in which it is currently reported, and all of the animals showed decreased adaptability relative to that of humans, except for mink. The neutrality plot showed that the effect of natural selection on different SARS-CoV-2 sequences is stronger than mutation pressure. A binding affinity analysis indicated that the spike protein of the SARS-CoV-2 variant in mink showed a greater preference for binding with the mink receptor ACE2 than with the human receptor, especially as the mutation Y453F and N501T in Mink-SARS2 lead to improvement of binding affinity for mink receptor. In summary, mutations Y453F and N501T in Mink-SARS2 lead to improvement of binding affinity with mink receptor, indicating possible natural selection and current host adaptation. Monitoring the variation and codon bias of SARS-CoV-2 provides a theoretical basis for tracing the epidemic, evolution and cross-species spread of SARS-CoV-2.

scholarly journals Analysis of synonymous codon usage bias and phylogeny of coat protein gene in banana bract mosaic virus isolates

VirusDisease ◽  
2017 ◽  
Vol 28 (2) ◽  
pp. 156-163 ◽  
Author(s):  
Atul B. Patil ◽  
Vijayendra S. Dalvi ◽  
Akhilesh A. Mishra ◽  
Bal Krishna ◽  
Abdul Azeez
Keyword(s):  
Coat Protein ◽  
Codon Usage ◽  
Mosaic Virus ◽  
Coat Protein Gene ◽  
Codon Usage Bias ◽  
Protein Gene ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Virus Isolates ◽  
Synonymous Codon Usage Bias

scholarly journals Analysis of Synonymous Codon Usage Bias in Chlamydia

2005 ◽  
Vol 37 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Hui Lü ◽  
Wei-Ming Zhao ◽  
Yan Zheng ◽  
Hong Wang ◽  
Mei Qi ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Synonymous Codon Usage Bias

scholarly journals Codon Usage Bias Analysis of Citrus tristeza Virus: Higher Codon Adaptation to Citrus reticulata Host

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 331 ◽  
Author(s):  
Kajal Biswas ◽  
Supratik Palchoudhury ◽  
Prosenjit Chakraborty ◽  
Utpal Bhattacharyya ◽  
Dilip Ghosh ◽  
...  
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Citrus Tristeza Virus ◽  
Synonymous Codon ◽  
Management Strategies ◽  
Bias Analysis ◽  
Mutation Pressure ◽  
Usage Patterns ◽  
Tristeza Virus ◽  
Citrus Tristeza

Citrus tristeza virus (CTV), a member of the aphid-transmitted closterovirus group, is the causal agent of the notorious tristeza disease in several citrus species worldwide. The codon usage patterns of viruses reflect the evolutionary changes for optimization of their survival and adaptation in their fitness to the external environment and the hosts. The codon usage adaptation of CTV to specific citrus hosts remains to be studied; thus, its role in CTV evolution is not clearly comprehended. Therefore, to better explain the host–virus interaction and evolutionary history of CTV, the codon usage patterns of the coat protein (CP) genes of 122 CTV isolates originating from three economically important citrus hosts (55 isolate from Citrus sinensis, 38 from C. reticulata, and 29 from C. aurantifolia) were studied using several codon usage indices and multivariate statistical methods. The present study shows that CTV displays low codon usage bias (CUB) and higher genomic stability. Neutrality plot and relative synonymous codon usage analyses revealed that the overall influence of natural selection was more profound than that of mutation pressure in shaping the CUB of CTV. The contribution of high-frequency codon analysis and codon adaptation index value show that CTV has host-specific codon usage patterns, resulting in higheradaptability of CTV isolates originating from C. reticulata (Cr-CTV), and low adaptability in the isolates originating from C. aurantifolia (Ca-CTV) and C. sinensis (Cs-CTV). The combination of codon analysis of CTV with citrus genealogy suggests that CTV evolved in C. reticulata or other Citrus progenitors. The outcome of the study enhances the understanding of the factors involved in viral adaptation, evolution, and fitness toward their hosts. This information will definitely help devise better management strategies of CTV.

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