title: Depletion of CpG Dinucleotides in Papillomaviruses and Polyomaviruses: A Role for Divergent Evolutionary Pressures.
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.
authors.affiliation: Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 006, India.
authors.forename: Mohita
authors.initials: M
authors.lastname: Upadhyay
authors.affiliation: Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 006, India.
authors.forename: Perumal
authors.initials: P
authors.lastname: Vivekanandan
mesh_terms: D000818:Animals; D003062:Codon / Q000235:genetics; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation; D018900:Dinucleotide Repeats / Q000235:genetics*; D019143:Evolution, Molecular; D006801:Humans; D009154:Mutation; D027383:Papillomaviridae / Q000235:genetics* / Q000502:physiology; D011120:Polyomavirus / Q000235:genetics* / Q000502:physiology
chemical_list: D003062:Codon