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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

CpT(ApG) depletion and CpG excess among large DNA viruses infecting invertebrate hosts.(a) Box plot showing the distribution of CpT(ApG) dinucleotides among large DNA viruses infecting invertebrate- and vertebrate hosts. The depletion of CpT(ApG) dinucleotides is more pronounced among large DNA viruses infecting invertebrates as compared to those infecting vertebrates (mean±SD: 0.72±0.10 vs 0.96±0.09; P<0.0001). (b) Box plot showing the distribution of CpG dinucleotides among large DNA viruses infecting invertebrate- and vertebrate hosts. Large DNA viruses infecting invertebrates had a significantly higher CpGO/E ratio than those infecting vertebrates (1.41±0.29 vs 0.99±0.26; P<0.0001).
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pone-0111793-g002: CpT(ApG) depletion and CpG excess among large DNA viruses infecting invertebrate hosts.(a) Box plot showing the distribution of CpT(ApG) dinucleotides among large DNA viruses infecting invertebrate- and vertebrate hosts. The depletion of CpT(ApG) dinucleotides is more pronounced among large DNA viruses infecting invertebrates as compared to those infecting vertebrates (mean±SD: 0.72±0.10 vs 0.96±0.09; P<0.0001). (b) Box plot showing the distribution of CpG dinucleotides among large DNA viruses infecting invertebrate- and vertebrate hosts. Large DNA viruses infecting invertebrates had a significantly higher CpGO/E ratio than those infecting vertebrates (1.41±0.29 vs 0.99±0.26; P<0.0001).

Mentions: The distribution of CpT(ApG) dinucleotides in large DNA viruses infecting invertebrates and vertebrates is shown in Figure 2a. Large DNA viruses infecting invertebrates had significantly lower CpT(ApG)O/E ratios than those infecting vertebrates (mean±SD:0.72±0.10 vs 0.96±0.09; P<0.0001). Large DNA viruses infecting invertebrates had a significantly higher CpGO/E ratios than those infecting vertebrates (1.41±0.29 vs 0.99±0.26; P<0.0001; Figure 2b). The distribution patterns of CpT and CpG dinucleotides are shown in Figure S1.


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)

CpT(ApG) depletion and CpG excess among large DNA viruses infecting invertebrate hosts.(a) Box plot showing the distribution of CpT(ApG) dinucleotides among large DNA viruses infecting invertebrate- and vertebrate hosts. The depletion of CpT(ApG) dinucleotides is more pronounced among large DNA viruses infecting invertebrates as compared to those infecting vertebrates (mean±SD: 0.72±0.10 vs 0.96±0.09; P<0.0001). (b) Box plot showing the distribution of CpG dinucleotides among large DNA viruses infecting invertebrate- and vertebrate hosts. Large DNA viruses infecting invertebrates had a significantly higher CpGO/E ratio than those infecting vertebrates (1.41±0.29 vs 0.99±0.26; P<0.0001).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111793-g002: CpT(ApG) depletion and CpG excess among large DNA viruses infecting invertebrate hosts.(a) Box plot showing the distribution of CpT(ApG) dinucleotides among large DNA viruses infecting invertebrate- and vertebrate hosts. The depletion of CpT(ApG) dinucleotides is more pronounced among large DNA viruses infecting invertebrates as compared to those infecting vertebrates (mean±SD: 0.72±0.10 vs 0.96±0.09; P<0.0001). (b) Box plot showing the distribution of CpG dinucleotides among large DNA viruses infecting invertebrate- and vertebrate hosts. Large DNA viruses infecting invertebrates had a significantly higher CpGO/E ratio than those infecting vertebrates (1.41±0.29 vs 0.99±0.26; P<0.0001).
Mentions: The distribution of CpT(ApG) dinucleotides in large DNA viruses infecting invertebrates and vertebrates is shown in Figure 2a. Large DNA viruses infecting invertebrates had significantly lower CpT(ApG)O/E ratios than those infecting vertebrates (mean±SD:0.72±0.10 vs 0.96±0.09; P<0.0001). Large DNA viruses infecting invertebrates had a significantly higher CpGO/E ratios than those infecting vertebrates (1.41±0.29 vs 0.99±0.26; P<0.0001; Figure 2b). The distribution patterns of CpT and CpG dinucleotides are shown in Figure S1.

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