Host and structure-specific codon usage of G genotype (VP7) among group A rotaviruses

Figures

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  Figure 1. Phylogenetic-tree analysis of RVA VP7. The maximum-likelihood method was used to construct the phylogenetic tree. Human, porcine, bovine, and bat RVA VP7 sequences are indicated by yellow, pink, green, and blue, respectively; 100 × bootstrap is represented in the phylogenetic-tree branches.

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  Figure 2. ENC-related analysis of RVA VP7. (A) Box line plot of ENC values for each strain from different hosts. Human, porcine, bovine, and bat RVA VP7 sequences are indicated by yellow, pink, green, and blue, respectively. (B) ENC plot of RVA, representing the relationship between ENC values and GC3 for each virulent strain. The solid curve plots the relationship between GC3s and ENC in the absence of selection pressure. ENC and GC3 scatters for most strains are evenly distributed below the standard curve. (C) Local zoomed in view of (B). Each scatter indicates ENC plot analysis results for the RVA strain. Yellow, pink, green, and blue scatter points indicate human, porcine, bovine, and bat RVA VP7 sequences, respectively. (D) Frequency distribution of ENC ratios for 172 sequences. ENC ratio was calculated as (ENC standard value − ENC value)/ENC standard value.

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  Figure 3. PR2 plot and neutral plot analyses of RVA VP7. (A) PR2 plot analysis of sequences of different host-coding areas of RVA. In the PR2 scatter plots, the points of all RVA strains are distributed in the upper-right quadrant and are relatively concentrated. (B) Local magnification of (A). (C–F) Neutral plot analysis of RVA VP7 (GC12 vs. GC3). The straight line represents the regression line; the regression equation is also shown. Slopes significantly deviating from 1 show evidence of natural selection, while slopes near 1 suggest mutational selection is the driving force of codon usage patterns.

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  Figure 4. Host synonymous codon usage and frequency of RV VP7 synonymous codon usage patterns. (A) Quantitative indicators of changes in amino acid synonymous codon usage patterns in different RVA hosts. Each scatter represents frequency of use of synonymous codons for each strain (yellow indicates human RVA VP7, pink indicates porcine RVA VP7, green indicates bovine RVA VP7, blue indicates bat RVA VP7). (B–E) The codon usage of the four host species. Represents the frequency of occurrence of amino acids per 1,000 triple codons. The names of the 20 amino acids are indicated by abbreviations.

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  Figure 5. CAI value (A) and RCDI (B) value of VP7 gene for four species: human, porcine, bovine, and bat.

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  Figure 6. Schematic of the structure of RVA VP7. Light gray regions 1–51 is the signal sequence. Dark gray regions 51–78 and 321–326 are the disordered N- and C-terminal arms, respectively. Red regions 78–161 and 256–321 are structural domain I; yellow regions 161–256 are structural domain II.

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  Figure 7. ENC values of nucleotide (nt) sequences corresponding to different structural domains of RVA VP7. (A,B) These two plots compare ENC values of nt sequences corresponding to structural domains I and II of different hosts. (C) Comparison of ENC values of corresponding nt sequences of different structural domains of the same host.