scholarly journals Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 81
Author(s):  
Hua Feng ◽  
Joaquim Segalés ◽  
Fangyu Wang ◽  
Qianyue Jin ◽  
Aiping Wang ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Large Scale ◽  
Codon Usage Pattern ◽  
Major Protein ◽  
Mutation Pressure ◽  
Coding Sequences ◽  
Usage Patterns ◽  
Porcine Circoviruses

Porcine circoviruses (PCVs) are distributed in swine herds worldwide and represent a threat to the health of domestic pigs and the profits of the swine industry. Currently, four PCV species, including PCV-1, PCV-2, PCV-3 and PCV-4, have been identified in China. Considering the ubiquitous characteristic of PCVs, the new emerged PCV-4 and the large scale of swine breeding in China, an overall analysis on codon usage bias for Chinese PCV sequences was performed by using the major proteins coding sequences (ORF1 and ORF2) to better understand the relationship of these viruses with their host. The data from genome nucleotide frequency composition and relative synonymous codon usage (RSCU) analysis revealed an overrepresentation of AT pair and the existence of a certain codon usage bias in all PCVs. However, the values of an effective number of codons (ENC) revealed that the bias was of low magnitude. Principal component analysis, ENC-plot, parity rule two analysis and correlation analysis suggested that natural selection and mutation pressure were both involved in the shaping of the codon usage patterns of PCVs. However, a neutrality plot revealed a stronger effect of natural selection than mutation pressure on codon usage patterns. Good host adaptation was also shown by the codon adaptation index analysis for all these viruses. Interestingly, obtained data suggest that PCV-4 might be more adapted to its host compared to other PCVs. The present study obtained insights into the codon usage pattern of PCVs based on ORF1 and ORF2, which further helps the understanding the molecular evolution of these swine viruses.

scholarly journals Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 604 ◽  
Author(s):  
Naveen Kumar ◽  
Diwakar Kulkarni ◽  
Benhur Lee ◽  
Rahul Kaushik ◽  
Sandeep Bhatia ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Similarity Index ◽  
Hendra Virus ◽  
Human Beings ◽  
Mutation Pressure ◽  
Usage Patterns ◽  
Adaptation Index

Hendra virus (HeV) and Nipah virus (NiV) are among a group of emerging bat-borne paramyxoviruses that have crossed their species-barrier several times by infecting several hosts with a high fatality rate in human beings. Despite the fatal nature of their infection, a comprehensive study to explore their evolution and adaptation in different hosts is lacking. A study of codon usage patterns in henipaviruses may provide some fruitful insight into their evolutionary processes of synonymous codon usage and host-adapted evolution. Here, we performed a systematic evolutionary and codon usage bias analysis of henipaviruses. We found a low codon usage bias in the coding sequences of henipaviruses and that natural selection, mutation pressure, and nucleotide compositions shapes the codon usage patterns of henipaviruses, with natural selection being more important than the others. Also, henipaviruses showed the highest level of adaptation to bats of the genus Pteropus in the codon adaptation index (CAI), relative to the codon de-optimization index (RCDI), and similarity index (SiD) analyses. Furthermore, a comparison to recently identified henipa-like viruses indicated a high tRNA adaptation index of henipaviruses for human beings, mainly due to F, G and L proteins. Consequently, the study concedes the substantial emergence of henipaviruses in human beings, particularly when paired with frequent exposure to direct/indirect bat excretions.

scholarly journals Comprehensive Analysis of Codon Usage on Porcine Astrovirus

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 991
Author(s):  
Huiguang Wu ◽  
Zhengyu Bao ◽  
Chunxiao Mou ◽  
Zhenhai Chen ◽  
Jingwen Zhao
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Similarity Index ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Broad Host Range ◽  
Mutation Pressure ◽  
Porcine Astrovirus ◽  
Usage Patterns

Porcine astrovirus (PAstV), associated with mild diarrhea and neurological disease, is transmitted in pig farms worldwide. The purpose of this study is to elucidate the main factors affecting codon usage to PAstVs. Phylogenetic analysis showed that the subtype PAstV-5 sat at the bottom of phylogenetic tree, followed by PAstV-3, PAstV-1, PAstV-2, and PAstV-4, indicating that the five existing subtypes (PAstV1-PAstV5) may be formed by multiple differentiations of PAstV ancestors. A codon usage bias was found in the PAstVs-2,3,4,5 from the analyses of effective number of codons (ENC) and relative synonymous codon usage (RSCU). Nucleotides A/U are more frequently used than nucleotides C/G in the genome CDSs of the PAstVs-3,4,5. Codon usage patterns of PAstV-5 are dominated by mutation pressure and natural selection, while natural selection is the main evolutionary force that affects the codon usage pattern of PAstVs-2,3,4. The analyses of codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) showed the codon usage similarities between the PAstV and animals might contribute to the broad host range and the cross-species transmission of astrovirus. Our results provide insight into understanding the PAstV evolution and codon usage patterns.

scholarly journals Genome-Wide Analysis of Codon Usage Patterns of SARS-CoV-2 Virus Reveals Global Heterogeneity of COVID-19

Biomolecules ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 912
Author(s):  
Saadullah Khattak ◽  
Mohd Ahmar Rauf ◽  
Qamar Zaman ◽  
Yasir Ali ◽  
Shabeen Fatima ◽  
...  
Keyword(s):  
Standard Deviation ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Geographic Location ◽  
Mutation Pressure ◽  
Genome Wide ◽  
Margin Of Error ◽  
Usage Patterns ◽  
Causative Agents ◽  
Virus Genomes

The ongoing outbreak of coronavirus disease COVID-19 is significantly implicated by global heterogeneity in the genome organization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The causative agents of global heterogeneity in the whole genome of SARS-CoV-2 are not well characterized due to the lack of comparative study of a large enough sample size from around the globe to reduce the standard deviation to the acceptable margin of error. To better understand the SARS-CoV-2 genome architecture, we have performed a comprehensive analysis of codon usage bias of sixty (60) strains to get a snapshot of its global heterogeneity. Our study shows a relatively low codon usage bias in the SARS-CoV-2 viral genome globally, with nearly all the over-preferred codons’ A.U. ended. We concluded that the SARS-CoV-2 genome is primarily shaped by mutation pressure; however, marginal selection pressure cannot be overlooked. Within the A/U rich virus genomes of SARS-CoV-2, the standard deviation in G.C. (42.91% ± 5.84%) and the GC3 value (30.14% ± 6.93%) points towards global heterogeneity of the virus. Several SARS-CoV-2 viral strains were originated from different viral lineages at the exact geographic location also supports this fact. Taking all together, these findings suggest that the general root ancestry of the global genomes are different with different genome’s level adaptation to host. This research may provide new insights into the codon patterns, host adaptation, and global heterogeneity of SARS-CoV-2.

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 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.

Expression levels and codon usage patterns in nuclear genes of the filarial nematodeWucheraria bancroftiand the blood flukeSchistosoma haematobium

2016 ◽  
Vol 91 (1) ◽  
pp. 72-79 ◽  
Author(s):  
G.A. Mazumder ◽  
A. Uddin ◽  
S. Chakraborty
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Evolutionary Relationship ◽  
Nuclear Genes ◽  
Codon Usage Pattern ◽  
Minor Role ◽  
Usage Pattern ◽  
Genetic Characteristics ◽  
Wide Range ◽  
Usage Patterns

AbstractSynonymous codons are used with different frequencies, a phenomenon known as codon bias, which exists in many genomes and is mainly resolute by mutation and selection. To elucidate the genetic characteristics and evolutionary relationship ofWucheraria bancroftiandSchistosoma haematobiumwe examined the pattern of synonymous codon usage in nuclear genes of both the species. The mean overall GC contents ofW. bancroftiandS. haematobiumwere 43.41 and 36.37%, respectively, which suggests that genes in both the species were AT rich. The value of the High Effective Number of Codons in both species suggests that codon usage bias was weak. Both species had a wide range of P3 distribution in the neutrality plot, with a significant correlation between P12 and P3. The codons were closer to the axes in correspondence analysis, suggesting that mutation pressure influenced the codon usage pattern in these species. We have identified the more frequently used codons in these species, most codons ending with an A or T. The nucleotides A/T and C/G were not proportionally used at the third position of codons, which reveals that natural selection might influence the codon usage patterns. The regression equation of P12 on P3 suggests that natural selection might have played a major role, while mutational pressure played a minor role in codon usage pattern in both species. These results form the basis of exploring the evolutionary mechanisms and the heterologous expression of medically important proteins ofW. bancroftiandS. haematobium.

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 Codon Usage Bias in Two Hemipteran Insect Species: Bemisia tabaci and Homalodisca coagulata

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Jyotika Sharma ◽  
Supriyo Chakraborty ◽  
Arif Uddin
Keyword(s):  
Codon Usage ◽  
Bemisia Tabaci ◽  
Codon Usage Bias ◽  
Codon Bias ◽  
Insect Species ◽  
Codon Usage Pattern ◽  
Mutation Pressure ◽  
Homalodisca Coagulata ◽  
Highly Expressed Genes ◽  
Hemipteran Insect

Codon bias is the nonuniform use of synonymous codons which encode the same amino acid. Some codons are more frequently used than others in several organisms, particularly in the highly expressed genes. The spectacular diversity of insects makes them a suitable candidate for analyzing the codon usage bias. Recent expansion in genome sequencing of different insect species provides an opportunity for studying the codon usage bias. Several works on patterns of codon usage bias were done on Drosophila and other related species but only few works were found in Hemiptera order. We analyzed codon usage in two Hemipteran insect species namely Bemisia tabaci and Homalodisca coagulata. Most frequent codons end with A or C at the 3rd codon position. The ENC (a measure of codon bias) value ranges from 43 to 60 (52.80) in B. tabaci but from 49 to 60 (56.69) in H. coagulata. In both insect species, a significant positive correlation was observed between A and A3%, C and C3%, and GC and GC3%, respectively. Our findings suggest that codon usage bias in two Hemipteran insect species is not remarkable and that mutation pressure causes the codon usage pattern in two Hemipteran insect species.

scholarly journals Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype

2021 ◽  
Vol 12 ◽  
Author(s):  
Fusheng Si ◽  
Li Jiang ◽  
Ruisong Yu ◽  
Wenqiang Wei ◽  
Zhen Li
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Porcine Epidemic Diarrhea Virus ◽  
Similarity Index ◽  
Host Adaptation ◽  
Economic Losses ◽  
Codon Usage Pattern ◽  
Diarrhea Virus ◽  
Porcine Epidemic Diarrhea

Porcine epidemic diarrhea virus (PEDV), which classified in the genus Alphacoronavirus, family Coronaviridae, is one of the most important pathogens that cause heavy economic losses in pig industry. Although intensive mutation and recombination analysis of PEDV strains were provided, systematic genome analysis were needed to elucidate the evolution mechanism and codon usage adaptation profiles of the pathogen. Here, a comprehensive investigation was carried out to reveal the systematic evolutionary processes of synonymous codon usage and host-adapted evolution phenotype of PEDV genome. We found a low codon usage bias (CUB) in PEDV genome and that nucleotide compositions, natural selection, mutation pressure and geographical diversity shapes the codon usage patterns of PEDV, with natural selection dominated the overall codon usage bias in PEDV than the others. By using the relative codon deoptimization index (RCDI) and similarity index (SiD) analysis, we observed that genotype II PEDV strains showed the highest level of adaptation phenotype to Sus scrofa than another divergent clade. To the best of our knowledge, this is the first comprehensive report elaborating the codon usage and host adaptation of PEDV. The findings offer an insight into our understanding of factors involved in PEDV evolution, adaptation and fitness toward their hosts.

scholarly journals A Comparison of Synonymous Codon Usage Bias Patterns in DNA and RNA Virus Genomes: Quantifying the Relative Importance of Mutational Pressure and Natural Selection

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Youhua Chen
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Total Variation ◽  
Codon Usage Bias ◽  
Rna Viruses ◽  
Gc Content ◽  
Relative Importance ◽  
Mutational Pressure ◽  
Dna And Rna ◽  
Usage Patterns

Codon usage bias patterns have been broadly explored for many viruses. However, the relative importance of mutation pressure and natural selection is still under debate. In the present study, I tried to resolve controversial issues on determining the principal factors of codon usage patterns for DNA and RNA viruses, respectively, by examining over 38000 ORFs. By utilizing variation partitioning technique, the results showed that 27% and 21% of total variation could be attributed to mutational pressure, while 5% and 6% of total variation could be explained by natural selection for DNA and RNA viruses, respectively, in codon usage patterns. Furthermore, the combined effect of mutational pressure and natural selection on influencing codon usage patterns of viruses is substantial (explaining 10% and 8% of total variation of codon usage patterns). With respect to GC variation, GC content is always negatively and significantly correlated with aromaticity. Interestingly, the signs for the significant correlations between GC, gene lengths, and hydrophobicity are completely opposite between DNA and RNA viruses, being positive for DNA viruses while being negative for RNA viruses. At last, GC12 versus G3s plot suggests that natural selection is more important than mutational pressure on influencing the GC content in the first and second codon positions.

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