Evolution and Genetic Diversity of Porcine Circovirus 3 in China

Figures

• 

  Figure 1. Map of PCV3 positive farms by country, and by province in China. Colored rectangles correspond to indicated PCV3 positive country and Chinese provinces. The yellow star indicates Fujian province.

• 

  Figure 2. Maximum likelihood trees based on full-length PCV3 sequences. Trees were reconstructed using RAxML (Version 8.4.10) with the general time reversible plus GAMMA (GTR + G) distribution substitution model (1000 bootstraps). Blue dots represent sequenced strains from this study. Colored lines indicate country or region of origin.

• 

  Figure 3. (A) Evolutionary rate for the PCV3 Cap gene. The evolutionary rate was estimated using BEAST (v1.8.4) with the GTR + G model and a relaxed lognormal molecular clock. The tree prior was set at coalescent: Bayesian skyline, and total chain length was 1 × 108 with sampling every 10,000 steps. (B) Bayesian skyline plot for the PCV3 Cap gene. The mean genetic diversity through time (Net) for the PCV3 ORF2 gene is shown by the black boldface line, while the 95% highest probability density (HPD) of Net is plotted on the y-axis (grey region).

• 

  Figure 4. Predicted structure of PCV3 Cap protein. Cap protein structure was predicted using I-TASSER (https://zhanglab.ccmb.med.umich.edu/I-TASSER/). The yellow filled circles indicate the epitope of PCV3 cap protein, the red filled circles indicate amino acids subjected to positive selection, and green lines indicate α-helixes and β-folds. (A) PCV3a (MF318452:PCV3-BJ-2), (B) PCV3b (KX458235:2164).