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

Upadhyay M, Vivekanandan P - PLoS ONE (2015)

Bottom Line: We analyzed the relative abundance of dinucleotides, effective codon number (ENC), differences in synonymous codon usage.CpG dinucleotide depletion was more pronounced among papillomaviruses and polyomaviruses infecting human and other mammals as compared to those infecting birds.The extent of CpG depletion among papillomaviruses and polyomaviruses is linked to the evolutionary lineage of the infected host.

View Article: PubMed Central - PubMed

Affiliation: Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 006, India.

ABSTRACT

Background: 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.

Methods: 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.

Results: 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.

Conclusions: 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.

No MeSH data available.


Related in: MedlinePlus

Role for mutational pressure in the evolution of papillomaviruses and polyomaviruses.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 (GC1,2) (Y-axis) among (a) papillomaviruses and (b) polyomaviruses. This finding suggests that mutational pressure contributes to the evolution of both papillomaviruses and polyomaviruses.
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pone.0142368.g004: Role for mutational pressure in the evolution of papillomaviruses and polyomaviruses.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 (GC1,2) (Y-axis) among (a) papillomaviruses and (b) polyomaviruses. This finding suggests that mutational pressure contributes to the evolution of both papillomaviruses and polyomaviruses.

Mentions: To investigate the role of mutational pressure in the evolution of papillomaviruses and polyomaviruses, we first analysed the correlation between GC content at first and second codon positions (GC1,2) and GC content at third codon position (GC3). Mutational pressure, if present will not act on specific codon positions and will therefore similarly affect GC1,2 and GC3. A good correlation between GC1,2 and GC3 implies a role for mutational pressure in virus evolution. We found a significant correlation between GC1,2 and GC3 among papillomaviruses (R2 = 0.429; P<0.0001; Fig 4a) and polyomaviruses (R2 = 0.385; P<0.0001; Fig 4b), suggesting that mutational pressure contributes to the evolution of both papillomaviruses and polyomaviruses.


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

Upadhyay M, Vivekanandan P - PLoS ONE (2015)

Role for mutational pressure in the evolution of papillomaviruses and polyomaviruses.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 (GC1,2) (Y-axis) among (a) papillomaviruses and (b) polyomaviruses. This finding suggests that mutational pressure contributes to the evolution of both papillomaviruses and polyomaviruses.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4636234&req=5

pone.0142368.g004: Role for mutational pressure in the evolution of papillomaviruses and polyomaviruses.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 (GC1,2) (Y-axis) among (a) papillomaviruses and (b) polyomaviruses. This finding suggests that mutational pressure contributes to the evolution of both papillomaviruses and polyomaviruses.
Mentions: To investigate the role of mutational pressure in the evolution of papillomaviruses and polyomaviruses, we first analysed the correlation between GC content at first and second codon positions (GC1,2) and GC content at third codon position (GC3). Mutational pressure, if present will not act on specific codon positions and will therefore similarly affect GC1,2 and GC3. A good correlation between GC1,2 and GC3 implies a role for mutational pressure in virus evolution. We found a significant correlation between GC1,2 and GC3 among papillomaviruses (R2 = 0.429; P<0.0001; Fig 4a) and polyomaviruses (R2 = 0.385; P<0.0001; Fig 4b), suggesting that mutational pressure contributes to the evolution of both papillomaviruses and polyomaviruses.

Bottom Line: We analyzed the relative abundance of dinucleotides, effective codon number (ENC), differences in synonymous codon usage.CpG dinucleotide depletion was more pronounced among papillomaviruses and polyomaviruses infecting human and other mammals as compared to those infecting birds.The extent of CpG depletion among papillomaviruses and polyomaviruses is linked to the evolutionary lineage of the infected host.

View Article: PubMed Central - PubMed

Affiliation: Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 006, India.

ABSTRACT

Background: 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.

Methods: 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.

Results: 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.

Conclusions: 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.

No MeSH data available.


Related in: MedlinePlus