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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

Lack of evidence for major codon usage biases.Correlation between GC content at third codon position (GC3) and the effective codon usage statistic (ENC) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts. The black line represents the expected ENC values (ENC*) calculated based on GC content. Most ENC values in both groups of viruses are on, or just below the ENC* values suggesting the absence of strong translational selection.
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pone-0111793-g004: Lack of evidence for major codon usage biases.Correlation between GC content at third codon position (GC3) and the effective codon usage statistic (ENC) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts. The black line represents the expected ENC values (ENC*) calculated based on GC content. Most ENC values in both groups of viruses are on, or just below the ENC* values suggesting the absence of strong translational selection.

Mentions: To investigate differences, if any in codon usage bias between the large DNA viruses infecting vertebrates and those infecting invertebrates we used the effective codon usage statistic, ENC (Effective number of codons) [11]. The ENC values ranged from 42.11 to 58.2 (mean±SD:53.77±4.02) for large DNA viruses infecting invertebrates and from 42.77 to 60.31 (mean±SD:54.83±4.58) for large DNA viruses infecting vertebrates. The ENC values clearly indicate the absence of major codon usage biases in both the groups of viruses. We examined the relationship between GC content at third codon position (GC3) and ENC values using ENC-GC3 plots. This relationship was then compared to the expected ENC value (ENC*) that would result if GC content primarily accounts for codon usage biases. In other words, ENC-GC3 plots will help assess the relative role of mutational pressure (ENC values lie on the expected ENC curve or just below the expected ENC curve) and translational selection (values would be considerably lower than the expected ENC curve). Interestingly, the actual values of ENC for both the groups of viruses lie on, or just below the expected ENC curve (Figure 4a and Figure 4b), indicating that codon usage bias is primarily explained by differences in GC composition and hence suggesting little or no role for translational selection.


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)

Lack of evidence for major codon usage biases.Correlation between GC content at third codon position (GC3) and the effective codon usage statistic (ENC) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts. The black line represents the expected ENC values (ENC*) calculated based on GC content. Most ENC values in both groups of viruses are on, or just below the ENC* values suggesting the absence of strong translational selection.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111793-g004: Lack of evidence for major codon usage biases.Correlation between GC content at third codon position (GC3) and the effective codon usage statistic (ENC) among (a) large DNA viruses infecting invertebrate hosts and (b) large DNA viruses infecting vertebrate hosts. The black line represents the expected ENC values (ENC*) calculated based on GC content. Most ENC values in both groups of viruses are on, or just below the ENC* values suggesting the absence of strong translational selection.
Mentions: To investigate differences, if any in codon usage bias between the large DNA viruses infecting vertebrates and those infecting invertebrates we used the effective codon usage statistic, ENC (Effective number of codons) [11]. The ENC values ranged from 42.11 to 58.2 (mean±SD:53.77±4.02) for large DNA viruses infecting invertebrates and from 42.77 to 60.31 (mean±SD:54.83±4.58) for large DNA viruses infecting vertebrates. The ENC values clearly indicate the absence of major codon usage biases in both the groups of viruses. We examined the relationship between GC content at third codon position (GC3) and ENC values using ENC-GC3 plots. This relationship was then compared to the expected ENC value (ENC*) that would result if GC content primarily accounts for codon usage biases. In other words, ENC-GC3 plots will help assess the relative role of mutational pressure (ENC values lie on the expected ENC curve or just below the expected ENC curve) and translational selection (values would be considerably lower than the expected ENC curve). Interestingly, the actual values of ENC for both the groups of viruses lie on, or just below the expected ENC curve (Figure 4a and Figure 4b), indicating that codon usage bias is primarily explained by differences in GC composition and hence suggesting little or no role for translational selection.

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