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Systematic CpT (ApG) depletion and CpG excess are unique genomic signatures of large DNA viruses infecting invertebrates.

Upadhyay M, Sharma N, Vivekanandan P - PLoS ONE (2014)

Bottom Line: We have identified systematic depletion of CpT(ApG) dinucleotides and over-representation of CpG dinucleotides as the unique genomic signature of large DNA viruses infecting invertebrates.Detailed investigation of this unique genomic signature suggests the existence of invertebrate host-induced pressures specifically targeting CpT(ApG) and CpG dinucleotides.The depletion of CpT dinucleotides among large DNA viruses infecting invertebrates is at least in part, explained by non-canonical DNA methylation by the infected host.

View Article: PubMed Central - PubMed

Affiliation: Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.

ABSTRACT
Differences in the relative abundance of dinucleotides, if any may provide important clues on host-driven evolution of viruses. We studied dinucleotide frequencies of large DNA viruses infecting vertebrates (n = 105; viruses infecting mammals = 99; viruses infecting aves = 6; viruses infecting reptiles = 1) and invertebrates (n = 88; viruses infecting insects = 84; viruses infecting crustaceans = 4). We have identified systematic depletion of CpT(ApG) dinucleotides and over-representation of CpG dinucleotides as the unique genomic signature of large DNA viruses infecting invertebrates. Detailed investigation of this unique genomic signature suggests the existence of invertebrate host-induced pressures specifically targeting CpT(ApG) and CpG dinucleotides. The depletion of CpT dinucleotides among large DNA viruses infecting invertebrates is at least in part, explained by non-canonical DNA methylation by the infected host. Our findings highlight the role of invertebrate host-related factors in shaping virus evolution and they also provide the necessary framework for future studies on evolution, epigenetics and molecular biology of viruses infecting this group of hosts.

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Related in: MedlinePlus

Neutrality plot.Evolution of large DNA viruses is primarily governed by mutational pressure. Scatter plot demonstrating a strong, near-perfect correlation between GC at the synonymous third codon position (GC3) (X-axis) and non-synonymous first/second codon positions (GC1,2) (Y-axis) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts. This finding suggesting that all codon positions are similarly affected and hence mutational pressure and not translational selection is primarily responsible for the observed differences in nucleotide composition among large DNA viruses.
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pone-0111793-g006: Neutrality plot.Evolution of large DNA viruses is primarily governed by mutational pressure. Scatter plot demonstrating a strong, near-perfect correlation between GC at the synonymous third codon position (GC3) (X-axis) and non-synonymous first/second codon positions (GC1,2) (Y-axis) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts. This finding suggesting that all codon positions are similarly affected and hence mutational pressure and not translational selection is primarily responsible for the observed differences in nucleotide composition among large DNA viruses.

Mentions: Nucleotide composition among the three codon positions in both group of viruses was further examined by comparing the GC content at the synonymous third position (GC3) with GC content at non-synonymous first and second codon position (GC1,2) (Figure 6a and 6b). The correlation between GC3 and GC1,2 is often used to understand the role of mutational pressure and/or translational selection influencing nucleotide composition. In our study, we found significant correlation between GC3 and GC1,2 in both the groups of viruses (r2 = 0.943 for large DNA viruses infecting invertebrates, P<0.0001, Figure 6a and r2 = 0.960 for those infecting vertebrates; P<0.0001, Figure 6b), implying that all codon positions are similarly affected.


Systematic CpT (ApG) depletion and CpG excess are unique genomic signatures of large DNA viruses infecting invertebrates.

Upadhyay M, Sharma N, Vivekanandan P - PLoS ONE (2014)

Neutrality plot.Evolution of large DNA viruses is primarily governed by mutational pressure. Scatter plot demonstrating a strong, near-perfect correlation between GC at the synonymous third codon position (GC3) (X-axis) and non-synonymous first/second codon positions (GC1,2) (Y-axis) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts. This finding suggesting that all codon positions are similarly affected and hence mutational pressure and not translational selection is primarily responsible for the observed differences in nucleotide composition among large DNA viruses.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4219779&req=5

pone-0111793-g006: Neutrality plot.Evolution of large DNA viruses is primarily governed by mutational pressure. Scatter plot demonstrating a strong, near-perfect correlation between GC at the synonymous third codon position (GC3) (X-axis) and non-synonymous first/second codon positions (GC1,2) (Y-axis) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts. This finding suggesting that all codon positions are similarly affected and hence mutational pressure and not translational selection is primarily responsible for the observed differences in nucleotide composition among large DNA viruses.
Mentions: Nucleotide composition among the three codon positions in both group of viruses was further examined by comparing the GC content at the synonymous third position (GC3) with GC content at non-synonymous first and second codon position (GC1,2) (Figure 6a and 6b). The correlation between GC3 and GC1,2 is often used to understand the role of mutational pressure and/or translational selection influencing nucleotide composition. In our study, we found significant correlation between GC3 and GC1,2 in both the groups of viruses (r2 = 0.943 for large DNA viruses infecting invertebrates, P<0.0001, Figure 6a and r2 = 0.960 for those infecting vertebrates; P<0.0001, Figure 6b), implying that all codon positions are similarly affected.

Bottom Line: We have identified systematic depletion of CpT(ApG) dinucleotides and over-representation of CpG dinucleotides as the unique genomic signature of large DNA viruses infecting invertebrates.Detailed investigation of this unique genomic signature suggests the existence of invertebrate host-induced pressures specifically targeting CpT(ApG) and CpG dinucleotides.The depletion of CpT dinucleotides among large DNA viruses infecting invertebrates is at least in part, explained by non-canonical DNA methylation by the infected host.

View Article: PubMed Central - PubMed

Affiliation: Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.

ABSTRACT
Differences in the relative abundance of dinucleotides, if any may provide important clues on host-driven evolution of viruses. We studied dinucleotide frequencies of large DNA viruses infecting vertebrates (n = 105; viruses infecting mammals = 99; viruses infecting aves = 6; viruses infecting reptiles = 1) and invertebrates (n = 88; viruses infecting insects = 84; viruses infecting crustaceans = 4). We have identified systematic depletion of CpT(ApG) dinucleotides and over-representation of CpG dinucleotides as the unique genomic signature of large DNA viruses infecting invertebrates. Detailed investigation of this unique genomic signature suggests the existence of invertebrate host-induced pressures specifically targeting CpT(ApG) and CpG dinucleotides. The depletion of CpT dinucleotides among large DNA viruses infecting invertebrates is at least in part, explained by non-canonical DNA methylation by the infected host. Our findings highlight the role of invertebrate host-related factors in shaping virus evolution and they also provide the necessary framework for future studies on evolution, epigenetics and molecular biology of viruses infecting this group of hosts.

Show MeSH
Related in: MedlinePlus