Differential Distributions of Mononucleotide Repeat Sequences in 256 Viral Genomes and Its Potential Implications

Gene. 2014 Jul 10;544(2):159-64. doi: 10.1016/j.gene.2014.04.063. Epub 2014 Apr 28.

Abstract

Mononucleotide repeats (MNRs) have been systematically investigated in the genomes of eukaryotic and prokaryotic organisms. However, detailed information on the distribution of MNRs in viral genomes is limited. In this study, we examined the distributions of MNRs in 256 fully sequenced virus genomes which showed extensive variations across viral genomes, and is significantly influenced by both genome size and CG content. Furthermore, the ratio of the observed to the expected number of MNRs (O/E ratio) appears to be influenced by both the host range and genome type of a particular virus. Additionally, the densities and frequencies of MNRs in genic regions are lower than in non-coding regions, suggesting that selective pressure acts on viral genomes. We also discuss the potential functional roles that these MNR loci could play in virus genomes. To our knowledge, this is the first analysis focusing on MNRs in viruses, and our study could have potential implications for a deeper understanding of virus genome stability and the co-evolution that occurs between a virus and its host.

Keywords: Evolution; Mononucleotide repeats; Virus genomes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Composition / genetics
  • Base Sequence
  • Chromosome Mapping
  • DNA, Viral / analysis
  • DNA, Viral / genetics*
  • Genetic Variation
  • Genome Size
  • Genome, Viral / genetics*
  • Host Specificity / genetics
  • Humans
  • Microsatellite Repeats / genetics*
  • Viruses / genetics*

Substances

  • DNA, Viral