Role for mutational pressure in the evolution of papillomaviruses and polyomaviruses.

<p>Scatter plot demonstrating a good correlation between GC content at the third codon position (GC₃) (X-axis) and GC content at first and second codon position (GC_1,2) (Y-axis) among (a) papillomaviruses and (b) polyomaviruses. This finding suggests that mutational pressure contributes to the evolution of both papillomaviruses and polyomaviruses.</p

Depletion of CpG Dinucleotides in Papillomaviruses and Polyomaviruses: A Role for Divergent Evolutionary Pressures

<div><p>Background</p><p>Papillomaviruses and polyomaviruses are small ds-DNA viruses infecting a wide-range of vertebrate hosts. Evidence supporting co-evolution of the virus with the host does not fully explain the evolutionary path of papillomaviruses and polyomaviruses. Studies analyzing CpG dinucleotide frequencies in virus genomes have provided interesting insights on virus evolution. CpG dinucleotide depletion has not been extensively studied among papillomaviruses and polyomaviruses. We sought to analyze the relative abundance of dinucleotides and the relative roles of evolutionary pressures in papillomaviruses and polyomaviruses.</p><p>Methods</p><p>We studied 127 full-length sequences from papillomaviruses and 56 full-length sequences from polyomaviruses. We analyzed the relative abundance of dinucleotides, effective codon number (ENC), differences in synonymous codon usage. We examined the association, if any, between the extent of CpG dinucleotide depletion and the evolutionary lineage of the infected host. We also investigated the contribution of mutational pressure and translational selection to the evolution of papillomaviruses and polyomaviruses.</p><p>Results</p><p>All papillomaviruses and polyomaviruses are CpG depleted. Interestingly, the evolutionary lineage of the infected host determines the extent of CpG depletion among papillomaviruses and polyomaviruses. CpG dinucleotide depletion was more pronounced among papillomaviruses and polyomaviruses infecting human and other mammals as compared to those infecting birds. Our findings demonstrate that CpG depletion among papillomaviruses is linked to mutational pressure; while CpG depletion among polyomaviruses is linked to translational selection. We also present evidence that suggests methylation of CpG dinucleotides may explain, at least in part, the depletion of CpG dinucleotides among papillomaviruses but not polyomaviruses.</p><p>Conclusions</p><p>The extent of CpG depletion among papillomaviruses and polyomaviruses is linked to the evolutionary lineage of the infected host. Our results highlight the existence of divergent evolutionary pressures leading to CpG dinucleotide depletion among small ds-DNA viruses infecting vertebrate hosts.</p></div

CpG dinucleotide frequencies in coding DNA sequences and non-coding sequences.

<p>CpG dinucleotide frequencies in coding DNA sequences and non-coding sequences.</p

Translational selection is more pronounced among polyomaviruses.

<p>Correlation between ENC values and GC₃ among (a) papillomaviruses (b) polyomaviruses. The red line represents the ENC expected value (ENC*) and blue diamonds represent the ENC values. The ENC values for papillomaviruses lie on, or just below the ENC expected curve whereas, the ENC values for polyomaviruses lie well below the ENC expected curve. (c) Box plots comparing the ENC values of papillomaviruses and polyomaviruses. Codon usage bias is more pronounced among polyomaviruses as compared to papillomaviruses as indicated by lower ENC values among polyomaviruses [49.74(95% CI of 48.87 to 50.61) vs 52.79 (95% CI of 52.06 to 53.54); P<0.0001]. (d) Box plots showing the differences between the expected ENC values (ENC*) and actual ENC values. The differences expected ENC values (ENC*) and actual ENC values were significantly higher among polyomaviruses as compared to papillomaviruses [7.30(95% CI of 6.86 to 7.75) vs 3.78 (95% CI of 3.54 to 4.03); P<0.0001]; this finding confirms increased codon usage bias or translational selection among polyomaviruses.</p

Relative abundance of dinucleotides in papillomaviruses and polyomaviruses.

<p>(a) The mean value for each dinucleotides O/E ratio (closed circles) are plotted for papillomaviruses. Among all the dinucleotide, CpG dinucleotides were clearly depleted among papillomaviruses (b) The mean value for each dinucleotides O/E ratio (closed circles) are plotted for polyomaviruses. CpG dinucleotide depletion is pronounced among polyomaviruses. (c) Among papillomaviruses, those infecting humans or other mammals (mammals other than humans) had significantly lower CpG O/E ratios than those infecting aves/reptiles [0.48 (95% CI of 0.47 to 0.5) vs 0.77(95% CI of 0.67 to 0.87); P<0.0001 and 0.51 (95% CI of 0.48 to 0.54) vs 0.77(95% CI of 0.67 to 0.87) P = 0.0004]. The relative abundance of CpG dinucleotides among papillomaviruses infecting humans was marginally lower than that of those infecting other mammals, this difference was not significant [0.48 (95% CI of 0.47 to 0.5) vs 0.51 (95% CI of 0.48 to 0.54), P = 0.1736]. (d) Polyomaviruses infecting humans were significantly CpG depleted as compared to those infecting other mammals [0.12(95% CI of 0.1 to 0.15) vs 0.20(95% CI of 0.16 to 0.24); P = 0.005] or aves [0.12(95% CI of 0.1 to 0.15) vs 0.44(95% CI of 0.3 to 0.57); P = 0.0007].</p

Role for depletion of CpG dinucleotides in the evolution of papillomaviruses and polyomaviruses.

<p>CpG dinucleotides are the most deviant (the difference between expected frequency and observed frequency) dinucleotides among papillomaviruses infecting (a) mammals (non-humans) (b) humans and (c) aves/reptiles. Similarly, CpG dinucleotides are the most deviant dinucleotides among polyomaviruses infecting (d) mammals (non-humans), (e) humans and (f) aves. This finding supports a major role for CpG dinucleotide depletion in the evolution of papillomaviruses and polyomaviruses across different host groups. Red color represents the deviation of CpG dinucleotides from 1 across all host groups of papillomaviruses and polyomaviruses.</p

Relative synonymous codon usage (RSCU) values of CpG-containing codons.

<p>Box plots showing the RSCU values of CpG-containing codons among (a) papillomaviruses and (b) polyomaviruses. CpG-containing codons are shown in red colour. The encoded amino acid is shown in parenthesis. Both group of viruses avoided CpG-containing synonymous codons as 100% (8 out of 8) of these codons had an RSCU value below one. (c) RSCU values of CpG-containing codons among papillomaviruses infecting different host groups: papillomaviruses infecting humans or other mammals had significantly lower RSCU values than those infecting aves/reptiles [0.47(95% CI of 0.42 to 0.52) vs 0.8(95% CI of 0.68 to 0.92); P = 0.0004; 0.55(95% CI of 0.53 to 0.58) vs 0.8(95% CI of 0.68 to 0.92); P = 0.0002]. (d) RSCU values of CpG-containing codons among polyomaviruses infecting different host groups: polyomaviruses infecting humans had significantly lower RSCU values as compared to those infecting other mammals [0.11(95% CI of 0.09 to 0.14) vs 0.17(95% CI of 0.16 to 0.19), P = 0.0007] or aves [0.11(95% CI of 0.09 to 0.14) vs 0.45(95% CI of 0.34 to 0.57); P = 0.0003].</p

Host methylation capabilitites may be linked to the depletion of CpT dinucleotides among large DNA viruses infecting invertebrates.

<p>(a) Scatter plot demonstrating a positive correlation between the loss of CpT dinucleotides (X-axis) and the gain of TpT dinucleotides (Y-axis) in large DNA viruses infecting invertebrate hosts. (b) There was no correlation between the loss of CpT dinucleotides (X-axis) and the gain of TpT dinucleotides (Y-axis) among large DNA viruses infecting vertebrate hosts. (c) Box plot showing the distribution of TpT dinucleotides among large DNA viruses infecting invertebrate and vertebrate hosts. The TpT_O/E ratios were significantly higher among the large DNA viruses infecting invertebrates as compared to those infecting vertebrates (mean±SD: 1.17±0.13 vs 1.08±0.11; <i>P</i><0.0001).</p

CpT(ApG) depletion and CpG excess among large DNA viruses infecting invertebrate hosts.

<p>(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; <i>P</i><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 CpG_O/E ratio than those infecting vertebrates (1.41±0.29 vs 0.99±0.26; <i>P</i><0.0001).</p

Systematic CpT (ApG) Depletion and CpG Excess Are Unique Genomic Signatures of Large DNA Viruses Infecting Invertebrates

<div><p>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.</p></div