scholarly journals Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus

2019 ◽  
Vol 20 (12) ◽  
pp. 2881 ◽  
Author(s):  
Gairu Li ◽  
Wenyan Zhang ◽  
Ruyi Wang ◽  
Gang Xing ◽  
Shilei Wang ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Sus Scrofa ◽  
Synonymous Codon ◽  
Dominant Role ◽  
Similarity Index ◽  
Control Measures ◽  
Sus Scrofa Domestica ◽  
Torque Teno Sus Virus

The torque teno sus virus (TTSuV) is an emerging virus threating the Suidae species of unclear pathogenicity, although it was previously reported as a worsening factor of other porcine diseases, in particular, porcine circovirus associated disease (PCVAD). Here, a comprehensive codon usage analysis of the open reading frame 1 (ORF1), which encodes the viral capsid protein, was undertaken for the first time to reveal its evolutionary history. We revealed independent phylogenetic processes for the two genera during TTSuV evolution, which was confirmed by principal component analysis (PCA). A low codon usage bias was observed in different genera and different species, with Kappatorquevirus a (TTSuVk2a) displaying the highest, which was mainly driven by mutation pressure and natural selection, especially natural selection. Overall, ATs were more abundant than GCs, along with more A-ended synonymous codons in relative synonymous codon usage (RSCU) analysis. To further confirm the role of natural selection and TTSuV adaptation to the Suidae species, codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses were performed, which showed different adaptations for different TTSuVs. Importantly, we identified a more dominant role of Sus scrofa in the evolution of Iotatorquevirus (TTSuV1), with the highest CAI values and lowest RCDI values compared to Sus scrofa domestica. However, in TTSuVk2, the roles of Sus scrofa and Sus scrofa domestica were the same, regarding codon usage, with similar CAI and RCDI values. Our study provides a new perspective of the evolution of TTSuV and valuable information to develop control measures against TTSuV.

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 Natural Selection Plays an Important Role in Shaping the Codon Usage of Structural Genes of the Viruses Belonging to the Coronaviridae Family

Viruses ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 3
Author(s):  
Dimpal A. Nyayanit ◽  
Pragya D. Yadav ◽  
Rutuja Kharde ◽  
Sarah Cherian
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Codon Position ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Structural Genes ◽  
Effective Number Of Codons ◽  
Neutrality Plot

Viruses belonging to the Coronaviridae family have a single-stranded positive-sense RNA with a poly-A tail. The genome has a length of ~29.9 kbps, which encodes for genes that are essential for cell survival and replication. Different evolutionary constraints constantly influence the codon usage bias (CUB) of different genes. A virus optimizes its codon usage to fit the host environment on which it savors. This study is a comprehensive analysis of the CUB for the different genes encoded by viruses of the Coronaviridae family. Different methods including relative synonymous codon usage (RSCU), an Effective number of codons (ENc), parity plot 2, and Neutrality plot, were adopted to analyze the factors responsible for the genetic evolution of the Coronaviridae family. Base composition and RSCU analyses demonstrated the presence of A-ended and U-ended codons being preferred in the 3rd codon position and are suggestive of mutational selection. The lesser ENc value for the spike ‘S’ gene suggests a higher bias in the codon usage of this gene compared to the other structural genes. Parity plot 2 and neutrality plot analyses demonstrate the role and the extent of mutational and natural selection towards the codon usage pattern. It was observed that the structural genes of the Coronaviridae family analyzed in this study were at the least under 84% influence of natural selection, implying a major role of natural selection in shaping the codon usage.

scholarly journals Evolution of Transmissible Gastroenteritis Virus (TGEV): A Codon Usage Perspective

2020 ◽  
Vol 21 (21) ◽  
pp. 7898
Author(s):  
Saipeng Cheng ◽  
Huiguang Wu ◽  
Zhenhai Chen
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Similarity Index ◽  
Transmissible Gastroenteritis Virus ◽  
Genotype I ◽  
Coding Sequence ◽  
Gastroenteritis Virus ◽  
Transmissible Gastroenteritis

Transmissible gastroenteritis virus (TGEV) is a coronavirus associated with diarrhea and high mortality in piglets. To gain insight into the evolution and adaptation of TGEV, a comprehensive analysis of phylogeny and codon usage bias was performed. The phylogenetic analyses of maximum likelihood and Bayesian inference displayed two distinct genotypes: genotypes I and II, and genotype I was classified into subtypes Ia and Ib. The compositional properties revealed that the coding sequence contained a higher number of A/U nucleotides than G/C nucleotides, and that the synonymous codon third position was A/U-enriched. The principal component analysis based on the values of relative synonymous codon usage (RSCU) showed the genotype-specific codon usage patterns. The effective number of codons (ENC) indicated moderate codon usage bias in the TGEV genome. Dinucleotide analysis showed that CpA and UpG were over-represented and CpG was under-represented in the coding sequence of the TGEV genome. The analyses of Parity Rule 2 plot, ENC-plot, and neutrality plot displayed that natural selection was the dominant evolutionary driving force in shaping codon usage preference in genotypes Ia and II. In addition, natural selection played a major role, while mutation pressure had a minor role in driving the codon usage bias in genotype Ib. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses suggested that genotype I might be more adaptive to pigs than genotype II. Current findings contribute to understanding the evolution and adaptation of TGEV.

scholarly journals Intragenomic variation in mutation biases causes underestimation of selection on synonymous codon usage

2021 ◽  
Author(s):  
Alexander L Cope ◽  
Premal Shah
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Codon Usage ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Mutation Bias ◽  
Biased Gene Conversion ◽  
Intragenomic Variation ◽  
The Impact

Patterns of non-uniform usage of synonymous codons (codon bias) varies across genes in an organism and across species from all domains of life. The bias in codon usage is due to a combination of both non-adaptive (e.g. mutation biases) and adaptive (e.g. natural selection for translation efficiency/accuracy) evolutionary forces. Most population genetics models quantify the effects of mutation bias and selection on shaping codon usage patterns assuming a uniform mutation bias across the genome. However, mutation biases can vary both along and across chromosomes due to processes such as biased gene conversion, potentially obfuscating signals of translational selection. Moreover, estimates of variation in genomic mutation biases are often lacking for non-model organisms. Here, we combine an unsupervised learning method with a population genetics model of synonymous codon bias evolution to assess the impact of intragenomic variation in mutation bias on the strength and direction of natural selection on synonymous codon usage across 49 Saccharomycotina budding yeasts. We find that in the absence of a priori information, unsupervised learning approaches can be used to identify regions evolving under different mutation biases. We find that the impact of intragenomic variation in mutation bias varies widely, even among closely-related species. We show that the overall strength and direction of selection on codon usage can be underestimated by failing to account for intragenomic variation in mutation biases. Interestingly, genes falling into clusters identified by machine learning are also often physically clustered across chromosomes, consistent with processes such as biased gene conversion. Our results indicate the need for more nuanced models of sequence evolution that systematically incorporate the effects of variable mutation biases on codon frequencies.

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 patterns in torque teno sus virus 1 (TTSuV1)

2012 ◽  
Vol 158 (1) ◽  
pp. 145-154 ◽  
Author(s):  
Zhicheng Zhang ◽  
Wei Dai ◽  
Yang Wang ◽  
Chengping Lu ◽  
Hongjie Fan
Keyword(s):  
Codon Usage ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Usage Patterns ◽  
Torque Teno Sus Virus

scholarly journals In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein?

2021 ◽  
Author(s):  
Tatyana Tikhomirova ◽  
Maxim Matyunin ◽  
Mikhail Lobanov ◽  
Oxana Galzitskaya
Keyword(s):  
Amino Acid ◽  
Codon Usage ◽  
Synonymous Codon ◽  
Dominant Role ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Mutational Pressure ◽  
Depth Analysis

Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. In turn, their amino acid composition remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage.

scholarly journals Natural Selection Determines Synonymous Codon Usage Patterns of Neuraminidase (NA) Gene of the Different Subtypes of Influenza A Virus in Canada

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Youhua Chen
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Influenza A Virus ◽  
Influenza A ◽  
Synonymous Codon ◽  
Phylogenetic Signal ◽  
Synonymous Codon Usage ◽  
Usage Patterns ◽  
Na Sequences ◽  
Na Gene

Synonymous codon usage patterns of neuraminidase (NA) gene of 64 subtypes (one is a mixed subtype) of influenza A virus found in Canada were analyzed. In total, 1422 NA sequences were analyzed. Among the subtypes, H1N1 is the prevailing one with 516 NCBI accession records, followed by H3N2, H3N8, and H4N6. The year of 2009 has the highest report records for the NA sequences in Canada, corresponding to the 2009 pandemic event. Correspondence analysis on the RSCU values of the four major subtypes showed that they had distinct clustering patterns in the two-dimensional scatter plot, indicating that different subtypes of IAV utilized different preferential codons. This subtype clustering pattern implied the important influence of natural selection, which could be further evidenced by an extremely flattened regression line in the neutrality plot (GC12 versus G3s plot) and a significant phylogenetic signal on the distribution of different subtypes in the clades of the phylogenetic tree (λ statistic). In conclusion, different subtypes of IAV showed an evolutionary differentiation on choosing different optimal codons. Natural selection played a deterministic role to structure IAV codon usage patterns in Canada.

scholarly journals Genetic Evolution and Molecular Selection of the HE Gene of Influenza C Virus

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 167 ◽  
Author(s):  
Wenyan Zhang ◽  
Letian Zhang ◽  
Wanting He ◽  
Xu Zhang ◽  
Baiqing Wen ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Similarity Index ◽  
Comparative Approach ◽  
Genetic Evolution ◽  
M Gene ◽  
Potential Threat ◽  
Mutation Pressure ◽  
Influenza C Virus ◽  
Molecular Selection

Influenza C virus (ICV) was first identified in humans and swine, but recently also in cattle, indicating a wider host range and potential threat to both the livestock industry and public health than was originally anticipated. The ICV hemagglutinin-esterase (HE) glycoprotein has multiple functions in the viral replication cycle and is the major determinant of antigenicity. Here, we developed a comparative approach integrating genetics, molecular selection analysis, and structural biology to identify the codon usage and adaptive evolution of ICV. We show that ICV can be classified into six lineages, consistent with previous studies. The HE gene has a low codon usage bias, which may facilitate ICV replication by reducing competition during evolution. Natural selection, dinucleotide composition, and mutation pressure shape the codon usage patterns of the ICV HE gene, with natural selection being the most important factor. Codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analysis revealed that the greatest adaption of ICV was to humans, followed by cattle and swine. Additionally, similarity index (SiD) analysis revealed that swine exerted a stronger evolutionary pressure on ICV than humans, which is considered the primary reservoir. Furthermore, a similar tendency was also observed in the M gene. Of note, we found HE residues 176, 194, and 198 to be under positive selection, which may be the result of escape from antibody responses. Our study provides useful information on the genetic evolution of ICV from a new perspective that can help devise prevention and control strategies.

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