Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species.

Viruses use the cellular machinery of their hosts for replication. It has therefore been proposed that the nucleotide and dinucleotide compositions of viruses should match those of their host species. If this is upheld, it may then be possible to use dinucleotide composition to predict the true host species of viruses sampled in metagenomic surveys. However, it is also clear that different taxonomic groups of viruses tend to have distinctive patterns of dinucleotide composition that may be independent of host species. To determine the relative strength of the effect of host versus virus family in shaping dinucleotide composition, we performed a comparative analysis of 20 RNA virus families from 15 host groupings, spanning two animal phyla and more than 900 virus species. In particular, we determined the odds ratios for the 16 possible dinucleotides and performed a discriminant analysis to evaluate the capability of virus dinucleotide composition to predict the correct virus family or host taxon from which it was isolated. Notably, while 81% of the data analyzed here were predicted to the correct virus family, only 62% of these data were predicted to their correct subphylum/class host and a mere 32% to their correct mammalian order. Similarly, dinucleotide composition has a weak predictive power for different hosts within individual virus families. We therefore conclude that dinucleotide composition is generally uniform within a virus family but less well reflects that of its host species. This has obvious implications for attempts to accurately predict host species from virus genome sequences alone.IMPORTANCE Determining the processes that shape virus genomes is central to understanding virus evolution and emergence. One question of particular importance is why nucleotide and dinucleotide frequencies differ so markedly between viruses. In particular, it is currently unclear whether host species or virus family has the biggest impact on dinucleotide frequencies and whether dinucleotide composition can be used to accurately predict host species. Using a comparative analysis, we show that dinucleotide composition has a strong phylogenetic association across different RNA virus families, such that dinucleotide composition can predict the family from which a virus sequence has been isolated. Conversely, dinucleotide composition has a poorer predictive power for the different host species within a virus family and across different virus families, indicating that the host has a relatively small impact on the dinucleotide composition of a virus genome.

Compositional biases and evolution of the largest plant RNA virus order Patatavirales.

Patatavirales is the largest order of plant RNA viruses and exclusively contains the family Potyviridae, accounting for 30 % of all known plant viruses. The composition bias of animal RNA viruses and several plant RNA viruses has been determined. However, the comprehensive nucleic acid composition, codon pair usage patterns, dinucleotide preference and codon pair preference of plant RNA viruses have not been investigated to date. In this study, integrated analysis and discussion of the nucleic acid composition, codon usage patterns, dinucleotide composition and codon pair bias of potyvirids were performed using 3732 complete genome coding sequences. The nucleic acid composition of potyvirids was significantly enriched in A/U. Interestingly, the A/U-rich nucleotide composition of Patatavirales is essential for determining the preferred A-ended and U-ended codons and the overexpression of UpG and CpA dinucleotides. The codon usage patterns and codon pair bias of potyvirids were significantly correlated with their nucleic acid composition. Additionally, the codon usage pattern, dinucleotide composition and codon-pair bias of potyvirids are more dependent on the classification of the virus compared with their hosts. Our analysis provides a better understanding of future research on the origin and evolution patterns of the order Patatavirales.

The dinucleotide composition of sugarcane mosaic virus is shaped more by protein coding regions than by host species.

Sugarcane mosaic virus (SCMV), which belongs to the Potyvirus genus of the family Potyviridae, causes mosaic diseases in canna, sugarcane and maize worldwide. Previously, the genetic variations, timescale, codon usage patterns and host adaptions of SCMV were determined. However, the dinucleotide composition and the dinucleotide bias from hosts or the protein coding regions of the virus have yet to be investigated. In this study, comprehensive analyses of the dinucleotide composition and dinucleotide bias from hosts, lineages and protein coding regions of SCMV were performed using 131 complete genomic sequences. We found that UpG and CpA were largely overrepresented while UpA, CpC, and CpG were largely underrepresented in the polyprotein and 11 protein coding region data sets. SCMV dinucleotide composition bias is more strongly dependent on the protein coding regions than on hosts. A weak association between the dinucleotide composition and SCMV lineages was also observed. Our analysis provides a novel perspective on the molecular evolutionary mechanisms of SCMV and may provide a better understanding of future research on the origin and evolutionary patterns of SCMV.

Synonymous Codon Pattern of Cowpea Mild Mottle Virus Sheds Light on Its Host Adaptation and Genome Evolution.

Cowpea mild mottle virus (CpMMV) is an economically significant virus that causes severe disease on several legume crops. Aside from recombination, other factors driving its rapid evolution are elusive. In this study, the synonymous codon pattern of CpMMV and factors shaping it were analyzed. Phylogeny and nucleotide composition analyses showed that isolates of different geography or hosts had very similar nucleotide compositions. Relative synonymous codon usage (RSCU) and neutrality analyses suggest that CpMMV prefers A/U-ending codons and natural selection is the dominative factor that affects its codon bias. Dinucleotide composition and codon adaptation analyses indicate that the codon pattern of CpMMV is mainly shaped by the requirement of escaping of host dinucleotide-associated antiviral responses and translational efficiency.

Analysis of synonymous codon usage in enterovirus 71.

Enterovirus 71 (EV71) is the major cause of hand-foot-and-mouth disease in children. In our study, using the complete genome sequences of 42 EV71 representing all three genotypes, we analyzed synonymous codon usage and the relative dinucleotide abundance in EV71 genome. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in EV71 genome. Furthermore, we observed that the relative abundance of dinucleotides in EV71 is independent of the overall base composition but is still the result of differential mutational pressure, which also shapes codon usage. In addition, other factors, such as hydrophobicity and aromaticity, also influence the codon usage variation among the genomes of EV71. This study represents the most comprehensive analysis of EV71 codon usage patterns and provides a basic understanding of the mechanisms for codon usage bias.