Genome dynamics and evolution of codon usage patterns in shrimp viruses

Tyagi, Anuj; Kumar, B. V. Sunil; Singh, Niraj Kumar

doi:10.1007/s00705-017-3445-7

Cited by 9 publications

(7 citation statements)

References 31 publications

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“…However, both viral genome and host mRNA are anticipated to share some common features due to constraint induced by host factors and their coexistence in the same cytoplasmic cellular environment (Kapoor et al, ). Coincidence in common under‐ and over‐represented codons between the virus and host, as well as antagonistic trend, was observed in this study, similar to previous reports (Biswas et al, ; Tyagi et al, ). The coincidence in common under‐ and over‐represented codons between the virus and its host may increase the translational efficiency of the corresponding protein (Butt, Nasrullah, & Tong, ).…”

Section: Discussionsupporting

confidence: 92%

“…The nucleotide composition at non‐synonymous and synonymous codon positions of RdRp and capsid of the nodavirus was analysed and compared in order to comprehend the properties and fundamental characteristic of the nodavirus genome. Due to the extreme divergence between RdRp and capsid of the mosinovirus (MoNV) that was reported recently (Domingo, Sheldon, & Perales, ; Schuster et al, ), the two RNA segments of the nodavirus were analysed separately in detail in the current analysis that is different from the previous studies (He & Teng, ; Kapoor, Simmonds, Lipkin, Zaidi, & Delwart, ; Schuster et al, ; Tyagi, Kumar, & Singh, ). The phylogenetic data classified MoNV as a novel member of alphanodavirus based on similar RdRp gene properties.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Comparative genome analysis reveals a distinct influence of nucleotide composition on virus–host species‐specific interaction of prawn‐infecting nodavirus

Ismail

Baharum

Fazry

et al. 2019

Journal of Fish Diseases

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Discovery of species‐specific interaction between the host and virus has drawn the interest of many researchers to study the evolution of the newly emerged virus. Comparative genome analysis provides insights of the virus functional genome evolution and the underlying mechanisms of virus–host interactions. The analysis of nucleotide composition signified the evolution of nodavirus towards host specialization in a host‐specific mutation manner. GC‐rich genome of betanodavirus was significantly deficient in UpA and UpU dinucleotides composition, whilst the AU‐rich genome of gammanodavirus was deficient in CpG dinucleotide. The capsid of MrNV and PvNV of gammanodavirus retains the highest abundance of adenine and uracil at the second codon position, respectively, which were found to be very distinctive from the other genera. ENC‐GC3 plot inferred the influence of natural selection and mutational pressure in shaping the evolution of MrNV RdRp and capsid, respectively. Furthermore, CAI/eCAI analysis predicts a comparable adaptability of MrNV in squid, Sepia officinalis than its natural host, Macrobrachium rosenbergii. Thus, further study is warranted to investigate the capacity of MrNV replication in S. officinalis owing to its high codon adaptation index.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Comparative genome analysis reveals a distinct influence of nucleotide composition on virus–host species‐specific interaction of prawn‐infecting nodavirus

Ismail

Baharum

Fazry

et al. 2019

Journal of Fish Diseases

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“…The maximum and minimum average ENC values were observed for Streptophyta (ENC 51.6 ± 3.2) and Actinobacteria (ENC 31.6 ± 5.3), respectively. Using the convention of 40 < ENC ≤ 55 to determine the degree of codon usage bias, 71,77,78 it can be assumed that Hsp60 genes of 17 phyla are highly and moderately biased. The Hsp60 genes from Group 1 (Apicomplexa, Firmicutes, and Bacteroidetes) with AT-mutation pressure and Group 4 (Ascomycota, Proteobacteria, Basidiomycota, Chlorophyta, and Actinobacteria) with GCmutation pressure have a high level of expression.…”

Section: Almost All Hsp60 Genes Have Lower Enc Values Than Expectedmentioning

confidence: 99%

In‐depth analysis of amino acid and nucleotide sequences of Hsp60: How conserved is this protein?

et al. 2022

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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. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s 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. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.

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“…Using the convention of 40 < ENC [?] 55 to determine the degree of codon usage bias 60,66,67 , it can be assumed that Hsp60 genes of 17 phyla are highly and moderately biased. The Hsp60 genes from Group 1 (Apicomplexa, Firmicutes, and Bacteroidetes) with AT-mutation pressure and Group 4 (Ascomycota, Proteobacteria, Basidiomycota, Chlorophyta, and Actinobacteria) with GC-mutation pressure have a high level of expression.…”

Section: Figurementioning

confidence: 99%

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

Tikhomirova

Matyunin

Лобанов

et al. 2021

Preprint

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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.

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Genome dynamics and evolution of codon usage patterns in shrimp viruses

Cited by 9 publications

References 31 publications

Comparative genome analysis reveals a distinct influence of nucleotide composition on virus–host species‐specific interaction of prawn‐infecting nodavirus

Comparative genome analysis reveals a distinct influence of nucleotide composition on virus–host species‐specific interaction of prawn‐infecting nodavirus

In‐depth analysis of amino acid and nucleotide sequences of Hsp60: How conserved is this protein?

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

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