Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts

Abstract

The genetic material of the three domains of life (Bacteria, Archaea, and Eukaryota) is always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) varies between ≈ 13% and ≈ 75%. Nucleotide composition is the simplest way of characterizing genomes. Despite this simplicity, it has several implications. Indeed, it is the main factor that determines, among other features, dinucleotide frequencies, repeated short DNA sequences, and codon and amino acid usage. Which forces drive this strong variation is still a matter of controversy. For rather obvious reasons, most of the studies concerning this huge variation and its consequences, have been done in free-living organisms. However, no recent comprehensive study of all known viruses has been done (that is, concerning all available sequences). Viruses, by far the most abundant biological entities on Earth, are the causative agents of many diseases. An overview of these entities is important also because their genetic material is not always double-stranded DNA: indeed, certain viruses have as genetic material single-stranded DNA, double-stranded RNA, single-stranded RNA, and/or retro-transcribing. Therefore, one may wonder if what we have learned about the evolution of GC content and its implications in prokaryotes and eukaryotes also applies to viruses. In this contribution, we attempt to describe compositional properties of ∼ 10,000 viral species: base composition (globally and according to Baltimore classification), correlations among non-coding regions and the three codon positions, and the relationship of the nucleotide frequencies and codon usage of viruses with the same feature of their hosts. This allowed us to determine how the base composition of phages strongly correlate with the value of their respective hosts, while eukaryotic viruses do not (with fungi and protists as exceptions). Finally, we discuss some of these results concerning codon usage: reinforcing previous results, we found that phages and hosts exhibit moderate to high correlations, while for eukaryotes and their viruses the correlations are weak or do not exist.

Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus

“…Variations in the composition of nucleotides can be a consequence of the adaptation of each viral species to the host organism. However, a recent study reported no correlation between the nucleotide composition of the pathogen and its host genome for eukaryotic viruses, in contrast to bacteriophages, for which such dependence was revealed [72], showing that changes in nucleotide composition for eukaryotic viruses may be caused by more complex adaptation processes.…”

Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus

“…Deciphering genomic nucleotide composition is a prerequisite for characterization of viral genomes [62]. Nucleotide composition at third codon sites is found unequal and nonrandom between species [63,64] and identification of major determining factors of SCUB is essential for understanding viral genome evolution [65].…”

Bias at the third nucleotide of codon pairs in virus and host genomes

“…This approach has been used to characterize viral genome bias with respect to the codon-pair frequencies of the human genome and to create attenuated viral genomes by recoding the genomes with codon pairs under-represented in the human genome 13 . However, there is variation in nucleotide content among different viral and host genomes 14 . More variation occurs at the third codon position than the second codon position as would be expected with the redundancy of the genetic code 14 .…”

“…However, there is variation in nucleotide content among different viral and host genomes 14 . More variation occurs at the third codon position than the second codon position as would be expected with the redundancy of the genetic code 14 . Codon-pair biases are influenced by both the dinucleotide spanning the codon-pair boundary and the tetranucleotide encompassing the second codon when the codon pair is positioned in the P and A sites of the ribosome 9 , 15 .…”