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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

Observed differences in codon usage bias are primarily explained by the differences in the background nucleotide composition.Graphs showing the relationship between GC content and the difference between ENC′ and ENC (i.e. ENC′-ENC) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts. For most viruses (except for one virus), the ENC′ values were greater than ENC values; implying that the observed differences in codon usage bias are further reduced when corrected for background nucleotide composition.
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pone-0111793-g005: Observed differences in codon usage bias are primarily explained by the differences in the background nucleotide composition.Graphs showing the relationship between GC content and the difference between ENC′ and ENC (i.e. ENC′-ENC) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts. For most viruses (except for one virus), the ENC′ values were greater than ENC values; implying that the observed differences in codon usage bias are further reduced when corrected for background nucleotide composition.

Mentions: The ENC statistic does not take into account the variation in nucleotide composition of the sequences studied [24]. ENC′ is a widely used statistic to measure codon usage bias and it takes into account the inherent differences in nucleotide composition of the sequence [24]. Higher the ENC′ values lower the codon usage bias. The ENC′ values ranged from 52.46 to 59.37 (mean±SD:56.74±1.68) for large DNA viruses infecting invertebrates and from 56.21 to 60.38 (mean±SD:59.23±0.93) for large DNA viruses infecting vertebrates. Notably, all ENC′ values (except for 1 virus) were higher than ENC values. This finding suggests that after correction for the observed background nucleotide composition there is no evidence of notable codon usage bias in either group of viruses studied. The difference between ENC′ values and ENC values (ENC′-ENC) are plotted against GC content in Figure 5a and 5b.


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)

Observed differences in codon usage bias are primarily explained by the differences in the background nucleotide composition.Graphs showing the relationship between GC content and the difference between ENC′ and ENC (i.e. ENC′-ENC) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts. For most viruses (except for one virus), the ENC′ values were greater than ENC values; implying that the observed differences in codon usage bias are further reduced when corrected for background nucleotide composition.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111793-g005: Observed differences in codon usage bias are primarily explained by the differences in the background nucleotide composition.Graphs showing the relationship between GC content and the difference between ENC′ and ENC (i.e. ENC′-ENC) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts. For most viruses (except for one virus), the ENC′ values were greater than ENC values; implying that the observed differences in codon usage bias are further reduced when corrected for background nucleotide composition.
Mentions: The ENC statistic does not take into account the variation in nucleotide composition of the sequences studied [24]. ENC′ is a widely used statistic to measure codon usage bias and it takes into account the inherent differences in nucleotide composition of the sequence [24]. Higher the ENC′ values lower the codon usage bias. The ENC′ values ranged from 52.46 to 59.37 (mean±SD:56.74±1.68) for large DNA viruses infecting invertebrates and from 56.21 to 60.38 (mean±SD:59.23±0.93) for large DNA viruses infecting vertebrates. Notably, all ENC′ values (except for 1 virus) were higher than ENC values. This finding suggests that after correction for the observed background nucleotide composition there is no evidence of notable codon usage bias in either group of viruses studied. The difference between ENC′ values and ENC values (ENC′-ENC) are plotted against GC content in Figure 5a and 5b.

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