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Deb B, Uddin A, Chakraborty S. Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae. Arch Virol 2021; 166:461-474. [PMID: 33392821 PMCID: PMC7779081 DOI: 10.1007/s00705-020-04890-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 10/02/2020] [Indexed: 01/31/2023]
Abstract
The present study was carried out on 62 genome sequences of members of the family Anelloviridae, as there have been no reports of genome analysis of these DNA viruses using a bioinformatics approach. The genes were found to be rich in AC content with low codon usage bias (CUB). Relative synonymous codon usage (RSCU) values identified the preferred codons for each amino acid in the family. The codon AGA was overrepresented, while the codons TCG, TTG, CGG, CGT, ACG, GCG and GAT were underrepresented in all of the genomes. A significant correlation was found between the effective number of codons (ENC) and base constraints, indicating that compositional properties might have influenced the CUB. A highly significant correlation was observed between the overall base content and the base content at the third codon position, indicating that mutations might have affected the CUB. A highly significant positive correlation was observed between GC12 and GC3 (r = 0.904, p < 0.01), which indicated that directional mutation pressure influenced all three codon positions. A neutrality plot revealed that the contribution of mutation and natural selection in determining the CUB was 58.6% and 41.4%, respectively.
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Affiliation(s)
- Bornali Deb
- Department of Biotechnology, Assam University, Silchar, Assam 788150 India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, Assam 788150 India
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Dutta R, Buragohain L, Borah P. Analysis of codon usage of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) and its adaptability in dog. Virus Res 2020; 288:198113. [PMID: 32771430 PMCID: PMC7410794 DOI: 10.1016/j.virusres.2020.198113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 01/10/2023]
Abstract
Codon analysis reveal natural selection and other undefined factors dominates the overall codon usage bias in SARS-CoV-2 rather than mutational pressure. The host adaptation potential of SARS-CoV-2 is more in human as compared to dog.
Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is recognized as one of the life-threatening viruses causing the most destructive pandemic in this century. The genesis of this virus is still unknown. To elucidate its molecular evolution and regulation of gene expression, the knowledge of codon usage is a pre-requisite. In this study, an attempt was made to document the genome-wide codon usage profile and the various factors influencing the codon usage patterns of SARS-CoV-2 in human and dog. The SARS-CoV-2 genome showed relative abundance of A and U nucleotides and relative synonymous codon usage analysis revealed that the preferred synonymous codons mostly end with A/U. The analysis of ENc-GC3s, Neutrality and Parity rule 2 plots indicated that natural selection and other undefined factors dominate the overall codon usage bias in SARS-CoV-2 whereas the impact of mutation pressure is comparatively minor. The codon adaptation index and relative codon deoptimization index of SARS-CoV-2 deciphered that human is more favoured host for adaptation compared to dog. These results enhance our understanding of the factors involved in evolution of the novel human SARS-CoV-2 and its adaptability in dog.
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Affiliation(s)
- Rupam Dutta
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati 22, Assam, India.
| | - Lukumoni Buragohain
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati 22, Assam, India
| | - Probodh Borah
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati 22, Assam, India
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Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus. Oncotarget 2017; 8:110337-110349. [PMID: 29299151 PMCID: PMC5746386 DOI: 10.18632/oncotarget.22738] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/27/2017] [Indexed: 11/25/2022] Open
Abstract
Middle East Respiratory Syndrome Coronavirus (MERS-CoV), which first broken out in Jeddah in 2012, causes a severe acute respiratory illness with a high mortality rate. To better understand the molecular characteristics of isolated MERS-CoV genomes, we first analysed the codon usage pattern of the zoonotic MERS-CoV strains comprehensively to gain an insight into the mechanism of cross-species transmission. We found that MERS human/camel isolates showed a low codon usage bias. Both mutation and nature selection pressure have contributed to this low codon usage bias, with the former being the main determining factor. We also observed that gene function, evolution time and the different host species of the virus all contributed to the bias of MERS-CoV, to some extent. Additionally, the codon usage pattern of MERS-CoV isolates is different from other related Nidovirales viruses isolated from bats and hedgehogs. In the future, more epidemiological surveys are required to examine the factors that resulted in the emergence and outbreak of this virus.
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Tian XT, Li BY, Zhang L, Jiao WQ, Liu JX. Bioinformatics analysis of rabbit haemorrhagic disease virus genome. Virol J 2011; 8:494. [PMID: 22044910 PMCID: PMC3377956 DOI: 10.1186/1743-422x-8-494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 11/01/2011] [Indexed: 11/10/2022] Open
Abstract
Background Rabbit haemorrhagic disease virus (RHDV), as the pathogeny of Rabbit haemorrhagic disease, can cause a highly infectious and often fatal disease only affecting wild and domestic rabbits. Recent researches revealed that it, as one number of the Caliciviridae, has some specialties in its genome, its reproduction and so on. Results In this report, we firstly analyzed its genome and two open reading frameworks (ORFs) from this aspect of codon usage bias. Our researches indicated that mutation pressure rather than natural is the most important determinant in RHDV with high codon bias, and the codon usage bias is nearly contrary between ORF1 and ORF2, which is maybe one of factors regulating the expression of VP60 (encoding by ORF1) and VP10 (encoding by ORF2). Furthermore, negative selective constraints on the RHDV whole genome implied that VP10 played an important role in RHDV lifecycle. Conclusions We conjectured that VP10 might be beneficial for the replication, release or both of virus by inducing infected cell apoptosis initiate by RHDV. According to the results of the principal component analysis for ORF2 of RSCU, we firstly separated 30 RHDV into two genotypes, and the ENC values indicated ORF1 and ORF2 were independent among the evolution of RHDV.
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Affiliation(s)
- Xiao-ting Tian
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujia ping 1, Yanchang bu, Lanzhou, Gansu, China
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Gu YX, Zhang J, Zhou JH, Zhao F, Liu WQ, Wang M, Chen HT, Ma LN, Ding YZ, Liu YS. Comparative analysis of ovine adenovirus 287 and human adenovirus 2 and 5 based on their codon usage. DNA Cell Biol 2011; 31:360-6. [PMID: 21810025 DOI: 10.1089/dna.2011.1256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ovine adenovirus 287 (OAdV287) emerges as one of the most promising gene vectors resulting from its unique biological characteristics. To obtain a more detailed knowledge about the codon usage of OAdV287, a comparative study based on the codon usage of OAdV287 and the prototypes of human adenovirus serotypes 2 and 5 (HAdV2/5) was carried out. Some commonly used indices measuring the codon usage patterns, including effective number of codons, relative synonymous codon usage, and statistical methods, were adopted. Overall, OAdV287 had a more biased and conservative codon usage pattern than that of HAdV2/5. Both mutation pressure and natural selection played important roles in shaping the codon usage patterns of these three adenoviruses. All the preference codons of OAdV287 had A/U ends and were totally different from those of sheep and humans; however, the preference codons of HAdV2/5 mostly had G/C ends and were mostly coincident with those of sheep and humans. The codon usage analysis in this study supplies some clues for further comprehending the unique biological characteristics of OAdV287 as gene vectors.
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Affiliation(s)
- Yuan-xing Gu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, PR China
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RoyChoudhury S, Mukherjee D. A detailed comparative analysis on the overall codon usage pattern in herpesviruses. Virus Res 2010; 148:31-43. [DOI: 10.1016/j.virusres.2009.11.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Revised: 11/27/2009] [Accepted: 11/30/2009] [Indexed: 11/30/2022]
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Evolution of the sequence composition of Flaviviruses. INFECTION GENETICS AND EVOLUTION 2010; 10:129-36. [DOI: 10.1016/j.meegid.2009.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 10/26/2009] [Accepted: 11/03/2009] [Indexed: 11/20/2022]
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Shi L, Li H, Ma G, Zhou J, Hong L, Zheng X, Wu Y, Wang Y, Yan Y. Competitive replication of different genotypes of infectious bursal disease virus on chicken embryo fibroblasts. Virus Genes 2008; 39:46-52. [DOI: 10.1007/s11262-008-0313-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2008] [Accepted: 11/28/2008] [Indexed: 10/21/2022]
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An extensive analysis on the global codon usage pattern of baculoviruses. Arch Virol 2008; 153:2273-82. [DOI: 10.1007/s00705-008-0260-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 10/27/2008] [Indexed: 12/18/2022]
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Analysis of synonymous codon usage in classical swine fever virus. Virus Genes 2008; 38:104-12. [PMID: 18958611 PMCID: PMC7089228 DOI: 10.1007/s11262-008-0296-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 10/09/2008] [Indexed: 01/27/2023]
Abstract
Using the complete genome sequences of 35 classical swine fever viruses (CSFV) representing all three genotypes and all three kinds of virulence, we analyzed synonymous codon usage and the relative dinucleotide abundance in CSFV. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in CSFV. Furthermore, we observed that the relative abundance of dinucleotides in CSFV is independent of the overall base composition but is still the result of differential mutational pressure, which also shapes codon usage. In addition, other factors, such as the subgenotypes and aromaticity, also influence the codon usage variation among the genomes of CSFV. This study represents the most comprehensive analysis to date of CSFV codon usage patterns and provides a basic understanding of the mechanisms for codon usage bias.
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Greenbaum BD, Levine AJ, Bhanot G, Rabadan R. Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PLoS Pathog 2008; 4:e1000079. [PMID: 18535658 PMCID: PMC2390760 DOI: 10.1371/journal.ppat.1000079] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 04/25/2008] [Indexed: 12/25/2022] Open
Abstract
It is well known that the dinucleotide CpG is under-represented in the genomic DNA of many vertebrates. This is commonly thought to be due to the methylation of cytosine residues in this dinucleotide and the corresponding high rate of deamination of 5-methycytosine, which lowers the frequency of this dinucleotide in DNA. Surprisingly, many single-stranded RNA viruses that replicate in these vertebrate hosts also have a very low presence of CpG dinucleotides in their genomes. Viruses are obligate intracellular parasites and the evolution of a virus is inexorably linked to the nature and fate of its host. One therefore expects that virus and host genomes should have common features. In this work, we compare evolutionary patterns in the genomes of ssRNA viruses and their hosts. In particular, we have analyzed dinucleotide patterns and found that the same patterns are pervasively over- or under-represented in many RNA viruses and their hosts suggesting that many RNA viruses evolve by mimicking some of the features of their host's genes (DNA) and likely also their corresponding mRNAs. When a virus crosses a species barrier into a different host, the pressure to replicate, survive and adapt, leaves a footprint in dinucleotide frequencies. For instance, since human genes seem to be under higher pressure to eliminate CpG dinucleotide motifs than avian genes, this pressure might be reflected in the genomes of human viruses (DNA and RNA viruses) when compared to those of the same viruses replicating in avian hosts. To test this idea we have analyzed the evolution of the influenza virus since 1918. We find that the influenza A virus, which originated from an avian reservoir and has been replicating in humans over many generations, evolves in a direction strongly selected to reduce the frequency of CpG dinucleotides in its genome. Consistent with this observation, we find that the influenza B virus, which has spent much more time in the human population, has adapted to its human host and exhibits an extremely low CpG dinucleotide content. We believe that these observations directly show that the evolution of RNA viral genomes can be shaped by pressures observed in the host genome. As a possible explanation, we suggest that the strong selection pressures acting on these RNA viruses are most likely related to the innate immune response and to nucleotide motifs in the host DNA and RNAs. Viruses are obligate intracellular parasites that use different strategies to sequester host cell machinery and avoid the host immune system. In this paper we explore the genomes of viruses that encode their genetic information in single-stranded RNA, a different material than the one used by their hosts (double-stranded DNA). It is interesting to observe that these viruses share some of the host's characteristics. For instance, one of the most underrepresented motifs in the DNA of vertebrates is the dinucleotide CpG. This is commonly thought to be due to methylation and deamination of cytosine residues in this dinucleotide. Surprisingly, the same CpG suppression is observed in vertebrate RNA viruses but not in RNA phages. We show that RNA viruses present similar dinucleotide pressures as their host genes. We find that the influenza A virus, which originated from an avian reservoir and replicated in humans over many generations, evolves to reduce the frequency of CpG dinucleotides mimicking the human genes. Influenza B, which has been in humans longer, exhibits an extremely low CpG dinucleotide content. These observations suggest that the evolution of RNA viruses is shaped by pressures observed in the host genome.
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Affiliation(s)
- Benjamin D. Greenbaum
- BioMaPS Institute, Rutgers University, Piscataway, New Jersey, United States of America
| | - Arnold J. Levine
- Institute for Advanced Study, Princeton, New Jersey, United States of America
| | - Gyan Bhanot
- BioMaPS Institute, Rutgers University, Piscataway, New Jersey, United States of America
- Institute for Advanced Study, Princeton, New Jersey, United States of America
| | - Raul Rabadan
- Institute for Advanced Study, Princeton, New Jersey, United States of America
- * E-mail:
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Woo PC, Wong BH, Huang Y, Lau SK, Yuen KY. Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Virology 2007; 369:431-42. [PMID: 17881030 PMCID: PMC7103290 DOI: 10.1016/j.virol.2007.08.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 08/02/2007] [Accepted: 08/07/2007] [Indexed: 12/01/2022]
Abstract
Using the complete genome sequences of 19 coronavirus genomes, we analyzed the codon usage bias, dinucleotide relative abundance and cytosine deamination in coronavirus genomes. Of the eight codons that contain CpG, six were markedly suppressed. The mean NNU/NNC ratio of the six amino acids using either NNC or NNU as codon is 3.262, suggesting cytosine deamination. Among the 16 dinucleotides, CpG was most markedly suppressed (mean relative abundance 0.509). No correlation was observed between CpG abundance and mean NNU/NNC ratio. Among the 19 coronaviruses, CoV-HKU1 showed the most extreme codon usage bias and extremely high NNU/NNC ratio of 8.835. Cytosine deamination and selection of CpG suppressed clones by the immune system are the two major independent biochemical and biological selective forces that shape codon usage bias in coronavirus genomes. The underlying mechanism for the extreme codon usage bias, cytosine deamination and G + C content in CoV-HKU1 warrants further studies.
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Affiliation(s)
- Patrick C.Y. Woo
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | | | - Yi Huang
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Susanna K.P. Lau
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- Department of Microbiology, The University of Hong Kong, Hong Kong
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong
- Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong
- Department of Microbiology, The University of Hong Kong, Hong Kong
- Corresponding author. State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Room 423, University Pathology Building, Queen Mary Hospital Compound, Pokfulam, Hong Kong. Fax: +852 2855 1241.
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