Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns

Figures

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  Figure 1. Phylogeny of segment 9 (VP7) of Rotavirus A colored by host species. Stars indicate avian-mammalian RVA spillover events (avian RVA to fox, avian RVA to raccoon, bovine RVA to turkeys). The alignment for this tree was made using complete VP7 sequences representing all known, available G types and hosts, to display the known-host range and host-boundary patterns for RVA. The VP7 (G) genotypes are labeled by clade. The tree file is available (SI file S1) with accession numbers for all sequences used. The phylogeny was run in BEAST v1.10.4 using a birth-death tree prior under an uncorrelated relaxed clock and a GTR+I+G substitution model, and the alignment was partitioned by translated and non-translated regions. Branch lengths correspond to substitutions.

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  Figure 2. Multi-dimensional scaling plot using 350 post-burn-in BEAST trees from each of the 11 RVA segments. Randomly sampled post-burn-in trees were taken from each segment to account for phylogenetic uncertainty. Points sharing the same color are from the same segment as shown in the legend. Points closer to each other indicate close geodesic distances and high levels of evolutionary linkage.

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  Figure 3. Time-scaled phylogenetic trees of Segments 1–3 for 789 mammalian RVA strains. The phylogenies are time-scaled using tip-dating. Scale bars below each tree represent branch length time in years. The branches are colored by rate. Cyan indicates the fastest evolutionary rate among all lineages, and black represents the slowest rate of evolution. Colored asterisks specify the host species the strain was isolated from as shown in the legend. Posterior probabilities, node bars for confidence intervals of the divergence dates, and tip labels for the strain names can be viewed by opening SI files S2–S4 (xml) or SI tree files S13–S15 in FigTree.

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  Figure 4. Time-scaled phylogenetic trees of Segments 4, 6, 9, and 5 for 789 mammalian RVA strains. Phylogenies are time-scaled using tip-dating. Scale bars below each tree represent branch length time in years. The branches are colored by rate. Cyan indicates the fastest evolutionary rate among all lineages, and black represents the slowest rate of evolution. Colored asterisks specify the host species the strain was isolated from as shown in Figure 3. Posterior probabilities, node bars for confidence intervals of the divergence dates and tip labels for the strain names can be viewed by opening SI files S5–S8 (xml) or SI tree files S16–S19 in FigTree.

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  Figure 5. Time-scaled phylogenetic trees of Segments 8, 7, 10, and 11 for 789 mammalian RVA strains. Phylogenies are time-scaled using tip-dating. Scale bars below each tree represent branch length time in years. Table 1. Posterior probabilities, node bars for confidence intervals of the divergence dates and tip labels for the strain names can be viewed in SI by opening SI files S9–S12 (xml) or tree files (SI 20–23) in FigTree.

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  Figure 6. Skyride plots of the 11 RVA segments. The X-axis represents the date. The Y-axis represent effective population size and is a proxy for genetic diversity. All segments show a sharp decrease in diversity roughly 10 years before 2017 (2006–2008).

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  Figure 7. Boxplots of the Codon Adaptation Index and Relative Codon Deoptimization Index values for RVA genes with respect to different RVA hosts. (A). Sampled sequences representing common genotypes for each of the 11 segments were measured for CAI with respect to the six hosts shown. The Y-axis value ranges are different for each host as some hosts have higher CAI values. Higher CAI values indicate more efficient expression. (B). RCDI values for the same sampled sequences from A plotted for each segment with respect to each host. RCDI values closest to 1 indicate more similar codon usage patterns. The Y-axis value ranges are different for each host. Tukey-Kramer 95% pair-wise confidence intervals are shown in SI Figure S3.

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  Figure 8. Tukey’s honest significance test for RCDI and CAI values between different host genomes. Values used for this test are the combined values for all segments used in Figure 6.

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  Figure 9. Neutrality plot of RVA ORFs. GC percentages of codon position 3 plotted against GC percentages of codon positions 1 and 2 (GC12) for the ORF for 11 RVA genes. Slopes significantly deviating from 1 show evidence of natural selection, while slopes near 1 suggest neutrality wherein mutational selection is the driving force of codon usage patterns.

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  Figure 10. Box plots of CAI and RCDI values for each ORF from strains isolated from specific hosts. RCDI and CAI values were derived by sampling 7 complete genomes (77 segment genomes) for each host, isolated from either avian (red), cow (green), human (blue), or pig (purple) hosts. These RVA genomes were then separately compared to cow, chicken, human or pig codon usage charts. ** if p < 0.01, *** if p < 0.001, **** if p < 0.0001, and ns if p > 0.05.