# Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns
## 3 Results
### Differing Codon Usage Patterns by Segment

Table 2: Mean rates, 95% highest posterior density (HPD), coefficient of variation, and date for the ‘time to most recent common ancestor’ (TMRCA) for each segment’s phylogenetic tree. 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. Synonymous Sites under Selection, However Evidence Does Not Suggest Translational Selection to Specific Hosts  
When comparing strains isolated from different species, there was no evidence to support the conclusion that RVAs adapt their codon usage to specific hosts (Figure 10). While the bovine strains and avian strains had RCDI values closer to 1.0 than the pig and human RVA strains, there were no significant differences between RCDI values of avian isolates compared to avian genomes vs. RCDI values of bovine isolates compared to avian genomes. Based on RCDI values, bovine strains were \"most compatible\" with avian genomes, and human strains were \"less compatible\" to the human genome than to bovine strains. Given that avian and mammalian RVAs do not exchange genetic information in nature, there is a substantial divergence between avian RVA isolates and mammalian RVA isolates. The fact that RVA strains show more similar codon patterns between bovine and  
Figure 8: [PERSON]’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.  
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. avian strains than between human and bovine strains suggests that translational selection by the host does not play a large role in codon bias. Rotavirus genes overall had higher CAI scores and lower RDCI scores when contrasted with the avian genome codon usage patterns (Figure 7). The lowest CAI and highest RDCI scores were observed when RVA genes were compared with rabbit genomes. However, there was little variation depending on which host the viral strain was isolated from (i.e., avian RVA strains did not have significantly different scores when compared to bovine RVA strains using the same reference codon usage patterns) (Figure 10). There was no evidence for detectable translational selection by the host, however, the observation that RVA was generally less optimized for the non-human mammalian genomes suggests that RVA may have higher protein expression levels in humans.