Figure 4

Genome-based comparisons of ΦCA82 and 14 other Microviridae. A) Comparisons of tetra-nucleotide frequencies as a measure of genome similarity at the nucleotide level. Boxplot represents the distributions of R² values for pairwise comparisons of tetra-nucleotide frequencies for each genome compared to all others. For each genome, the closest match (highest R²) is shown to the right. B) Genomic sequence similarity as assessed by clustering of predicted amino-acid sequences. Clustering was completed with CD-HIT as described in the text, which accomplishes an all-versus-all comparison of each predicted protein. Sequence clusters were determined with a 40% similarity cutoff (sequences must be >40% similar for membership within the same cluster); tree is based on cluster memberships across all genomes. C) Genomic functional similarity as assessed by gene counts for each genome in pfam categories as classified by IMG. Tree construction methodology is essentially identical to (B), but based on functional cluster membership rather than clustering based on sequence similarity. D) Shared and unique predicted genes between ΦCA82 and all 14 other Microviridae members as determined by the CD-HIT clustering used for (B) and BLAST as described in the text.