# Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns
## 3 Results
### Differing Codon Usage Patterns by Segment  
Compared to the other ORFs, NSP5 possessed significantly higher CAI scores and significantly lower RCDI scores across all host genomes. The wide range of values for each RVA segment suggests that, while there may be differences in selective pressure on codon usage by segment, the translational selection was relatively weak compared to mutational selection for the rest of the genome. Codon usage patterns for both mammalian and avian RVA appear more compatible with avian genomes than mammalian genomes (Figures 7 and 8), however, human genomes and avian genomes showed similar compatibility between one another, with RVA genomes, and their CAI scores were not significantly different. RVA had higher CAI values and RCDI scores closer to 1 for both human and avian genomes relative to rabbit, cow, pig, and dog genomes. RVA compared against the pig genome resulted in the lowest CAI scores for all segments and strains. In other words, based on CAI and RCDI metrics, RVA is predicted to be the least translationally efficient within pigs. A neutrality plot revealed that NSP4 had the highest GC content in position 3 (GC3) relative to the other segments. VP6 had the highest GC content in positions 1 and 2 (GC12) relative to the other segments while NSP1 and VP3 had the lowest GC12 content. While VP6's GC12 content was higher than the rest of the RVA genome, VP6's GC3 content was not. The slopes for all regression lines deviated from 1 (Figure 9), ranging from 0.043 (VP7) to 0.316 (NSP1), indicating that there was significant selective pressure on position 3 for codon usage for all segments. The slopes indicate NSP1 is under more mutational pressure than the other segments, while VP7 is under more selective pressure at position 3 compared with the other segments, however, the lower GC3 values relative to GC12 in VP7 actually indicates _lower_ adaptation to the host genome. The lower GC3 values relative to GC12 in VP1 and VP3 also showed low slopes (0.06 and 0.05 respectively), suggesting that they may also be under less mutation pressure and more translational selection, however like VP7, the relatively low GC3 content in already high AU genome, suggests the translational efficiency would be lower. The correlation coefficient overall for GC12 and GC3 was 0.261 (\(p<0.001\)). While some segments/ORFs (VP1, VP2, VP4, NSP1, NSP2, NSP3, and NSP5) were more significantly positively correlated between GC12 and GC3, segments 9 and 10 displayed no significant correlation. \begin{table}
\begin{tabular}{c c c c c c} \hline \hline
**Segment** & **Mean Rate** & \multicolumn{2}{c}{**95\% HPD**} & \multicolumn{2}{c}{**Coefficient of**} & \\  & & **(Lower, Upper)** & **Variation** & **TMRCA** \\ \hline Segment 1 (VP1) & \(1.724\times 10^{-3}\) & \(1.610\times 10^{-3}\) & \(1.835\times 10^{-3}\) & 2.410 & 1957 \\ Segment 2 (VP2) & \(1.703\times 10^{-3}\) & \(1.589\times 10^{-3}\) & \(1.826\times 10^{-3}\) & 2.602 & 1963 \\ Segment 3 (VP3) & \(1.948\times 10^{-3}\) & \(1.814\times 10^{-3}\) & \(2.087\times 10^{-3}\) & 2.436 & 1962 \\ Segment 4 (VP4) & \(3.775\times 10^{-3}\) & \(3.517\times 10^{-3}\) & \(4.044\times 10^{-3}\) & 8.978 & 1964.5 \\ Segment 5 (NSP1) & \(2.953\times 10^{-3}\) & \(2.694\times 10^{-3}\) & \(3.223\times 10^{-3}\) & 3.994 & 1964.5 \\ Segment 6 (VP6) & \(1.694\times 10^{-3}\) & \(1.541\times 10^{-3}\) & \(1.857\times 10^{-3}\) & 3.412 & 1967.5 \\ Segment 7 (NSP3) & \(1.615\times 10^{-3}\) & \(1.454\times 10^{-3}\) & \(1.778\times 10^{-3}\) & 5.061 & 1967 \\ Segment 8 (NSP2) & \(1.473\times 10^{-3}\) & \(1.335\times 10^{-3}\) & \(1.610\times 10^{-3}\) & 3.323 & 1966.5 \\ Segment 9 (VP7) & \(2.660\times 10^{-3}\) & \(2.400\times 10^{-3}\) & \(2.940\times 10^{-3}\) & 3.375 & 1966.5 \\ Segment 10 (NSP4) & \(1.583\times 10^{-3}\) & \(1.420\times 10^{-3}\) & \(1.743\times 10^{-3}\) & 2.599 & 1967.5 \\ Segment 11 (NSP5/6) & \(2.424\times 10^{-3}\) & \(2.040\times 10^{-3}\) & \(2.831\times 10^{-3}\) & 3.285 & 1969 \\ \hline \hline \end{tabular}
\end{table}