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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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Invertebrate host-induced pressure is specific to CpT (and not TpC) and CpG (and not GpC) dinucleotides.(a) Box plot comparing the CpTO/E/TpCO/E ratios among large DNA viruses infecting invertebrates and vertebrates. The CpTO/E/TpCO/E ratios were significantly lower in large DNA viruses infecting invertebrates as compared to those infecting vertebrates (0.76±0.11 vs 0.93±0.14; P<0.0001) clearly demonstrating that CpT dinucleotides but not TpC dinucleotides are subjected to host-induced pressures. (b) Box plot comparing the relative CpGO/E/GpCO/E ratios dinucleotides among large DNA viruses infecting invertebrates and vertebrates. The CpGO/E/GpCO/E ratios among large DNA viruses infecting invertebrates were significantly higher than those infecting vertebrates (1.17±0.32 vs 1.06±0.28; P = 0.01), demonstrating that CpG dinucleotides but not GpC dinucleotides are subjected to host-induced pressures among large DNA viruses infecting invertebrate hosts.
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pone-0111793-g007: Invertebrate host-induced pressure is specific to CpT (and not TpC) and CpG (and not GpC) dinucleotides.(a) Box plot comparing the CpTO/E/TpCO/E ratios among large DNA viruses infecting invertebrates and vertebrates. The CpTO/E/TpCO/E ratios were significantly lower in large DNA viruses infecting invertebrates as compared to those infecting vertebrates (0.76±0.11 vs 0.93±0.14; P<0.0001) clearly demonstrating that CpT dinucleotides but not TpC dinucleotides are subjected to host-induced pressures. (b) Box plot comparing the relative CpGO/E/GpCO/E ratios dinucleotides among large DNA viruses infecting invertebrates and vertebrates. The CpGO/E/GpCO/E ratios among large DNA viruses infecting invertebrates were significantly higher than those infecting vertebrates (1.17±0.32 vs 1.06±0.28; P = 0.01), demonstrating that CpG dinucleotides but not GpC dinucleotides are subjected to host-induced pressures among large DNA viruses infecting invertebrate hosts.

Mentions: The CpT dinucleotide is amenable to methylation, while the TpC dinucleotide is not. We investigated the CpTO/E/TpCO/E ratios for the viruses studied. The CpTO/E/TpCO/E ratios were significantly lower in large DNA viruses infecting invertebrates as compared to those infecting vertebrates (0.76±0.11 vs 0.93±0.14; P<0.0001; Figure 7a), clearly demonstrating that CpT dinucleotides but not TpC dinucleotides are amenable to invertebrate host-induced substitutions. Similarly, the CpGO/E/GpCO/E ratios among large DNA viruses infecting invertebrates were significantly higher than those infecting vertebrates (1.17±0.32 vs1.06±0.28; P = 0.01; Figure 7b).


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)

Invertebrate host-induced pressure is specific to CpT (and not TpC) and CpG (and not GpC) dinucleotides.(a) Box plot comparing the CpTO/E/TpCO/E ratios among large DNA viruses infecting invertebrates and vertebrates. The CpTO/E/TpCO/E ratios were significantly lower in large DNA viruses infecting invertebrates as compared to those infecting vertebrates (0.76±0.11 vs 0.93±0.14; P<0.0001) clearly demonstrating that CpT dinucleotides but not TpC dinucleotides are subjected to host-induced pressures. (b) Box plot comparing the relative CpGO/E/GpCO/E ratios dinucleotides among large DNA viruses infecting invertebrates and vertebrates. The CpGO/E/GpCO/E ratios among large DNA viruses infecting invertebrates were significantly higher than those infecting vertebrates (1.17±0.32 vs 1.06±0.28; P = 0.01), demonstrating that CpG dinucleotides but not GpC dinucleotides are subjected to host-induced pressures among large DNA viruses infecting invertebrate hosts.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111793-g007: Invertebrate host-induced pressure is specific to CpT (and not TpC) and CpG (and not GpC) dinucleotides.(a) Box plot comparing the CpTO/E/TpCO/E ratios among large DNA viruses infecting invertebrates and vertebrates. The CpTO/E/TpCO/E ratios were significantly lower in large DNA viruses infecting invertebrates as compared to those infecting vertebrates (0.76±0.11 vs 0.93±0.14; P<0.0001) clearly demonstrating that CpT dinucleotides but not TpC dinucleotides are subjected to host-induced pressures. (b) Box plot comparing the relative CpGO/E/GpCO/E ratios dinucleotides among large DNA viruses infecting invertebrates and vertebrates. The CpGO/E/GpCO/E ratios among large DNA viruses infecting invertebrates were significantly higher than those infecting vertebrates (1.17±0.32 vs 1.06±0.28; P = 0.01), demonstrating that CpG dinucleotides but not GpC dinucleotides are subjected to host-induced pressures among large DNA viruses infecting invertebrate hosts.
Mentions: The CpT dinucleotide is amenable to methylation, while the TpC dinucleotide is not. We investigated the CpTO/E/TpCO/E ratios for the viruses studied. The CpTO/E/TpCO/E ratios were significantly lower in large DNA viruses infecting invertebrates as compared to those infecting vertebrates (0.76±0.11 vs 0.93±0.14; P<0.0001; Figure 7a), clearly demonstrating that CpT dinucleotides but not TpC dinucleotides are amenable to invertebrate host-induced substitutions. Similarly, the CpGO/E/GpCO/E ratios among large DNA viruses infecting invertebrates were significantly higher than those infecting vertebrates (1.17±0.32 vs1.06±0.28; P = 0.01; Figure 7b).

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