Figure legends:
Figure 1 Size and amino acid sequence differences of 90cap proteins obtained in this study. Bars indicating thecap proteins are filled according to the phylogenetic group they occupy. The upper bar represents the consensus of the known PiCVcap proteins; Amino acids are numbered from 1 to 277. Gaps indicate the location of deleted (compared to the consensus sequence) amino acids. The number on the right is the length of capproteins.
Figure 2 Comparison of the amino acid sequence conservation at a particular position between the 90 identified PiCV strains and the PiCV reference strains available in GenBank. (a) The 90 identified PiCV strains from the racing pigeons in China. (b) The 54 Chinese PiCV reference strains available in GenBank. (c) The 72 PiCV reference strains available in GenBank from other countries. Note. The GenBank accession no. of the 90 identified PiCV strains, the 54 Chinese PiCV reference strains and 72 PiCV reference strains from other countries was shown in Table 2, S1 and S2.
Figure 3 Divergence analysis of cap proteins of the 90 identified PiCV strains. (a) The 90 identified PiCV strains from the racing pigeons in China. (b) The 54 Chinese PiCV reference strains available in GenBank. (c) The 72 PiCV reference strains available in GenBank from other countries. The unique amino acid mutations found in this study are indicated in red. Note. All PiCV reference strains were the same to the Figure 2.
Figure 4 Phylogenetic analysis of PiCV strains based on 90cap gene sequences identified in this study and 126 capgene sequences available in GeneBank. A maximum likelihood phylogenetic tree was automatically constructed with 1000 bootstrap replicates and the remaining default parameters in the MEGA 5.0 software, and the Interactive Tree Of Life (iTOL) software was used for the display and annotation of the phylogenetic tree. Labels at branch tips refer to the strain name and GenBank accession number. Red taxa highlight the 90 PiCV genome sequences isolated from the racing pigeons geographically located in China.
Figure 5 Recombination breakpoint distribution plots for 67 PiCV full genome sequences identified in this study and 113 PiCV full genome sequences available in GenBank. The red and blue areas of the plots indicate recombination breakpoint hot-spots and cold-spots, respectively. The dark and light grey areas represent the 95% and 99% confidence intervals of the expected degrees of breakpoint clustering under random recombination, respectively.