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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

CpGO/E ratios are not influenced by GC content.Scatter plot demonstrating the lack of correlation between CpGO/E ratios (X-axis) and GC content (Y-axis) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts.
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pone-0111793-g003: CpGO/E ratios are not influenced by GC content.Scatter plot demonstrating the lack of correlation between CpGO/E ratios (X-axis) and GC content (Y-axis) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts.

Mentions: The GC content ranged from 19–58% in large DNA viruses infecting invertebrate hosts and between 26–77% in those infecting vertebrate hosts. A positive correlation between GC content and CpG dinucleotide frequencies has been demonstrated in previous studies [25], [26]. In our study, there was no correlation between CpGO/E ratios and GC content (Figure 3a: r2 = 0.057; P = 0.226 for the large DNA viruses infecting invertebrates; and Figure 3b: r2 = 0.017; P = 0.182 for large DNA viruses infecting vertebrates).


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)

CpGO/E ratios are not influenced by GC content.Scatter plot demonstrating the lack of correlation between CpGO/E ratios (X-axis) and GC content (Y-axis) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111793-g003: CpGO/E ratios are not influenced by GC content.Scatter plot demonstrating the lack of correlation between CpGO/E ratios (X-axis) and GC content (Y-axis) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts.
Mentions: The GC content ranged from 19–58% in large DNA viruses infecting invertebrate hosts and between 26–77% in those infecting vertebrate hosts. A positive correlation between GC content and CpG dinucleotide frequencies has been demonstrated in previous studies [25], [26]. In our study, there was no correlation between CpGO/E ratios and GC content (Figure 3a: r2 = 0.057; P = 0.226 for the large DNA viruses infecting invertebrates; and Figure 3b: r2 = 0.017; P = 0.182 for large DNA viruses infecting vertebrates).

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