Figure 2

Genetic diversity and selective pressure in the HRVA and HRVB genomes. A. HRV genome organization. Genome schematic depicting genes in coding regions (boxes) and the non-coding regions (lines). Black bars above genome schematic indicate classes of gene products and gene product identities, where known VP = viral protein; PRO = viral protease; ATPase = DEXH-box ATPase protein; VPg = viral protein genomic (highlighted by dotted box); POL = RNA dependent RNA polymerase; NCR = non-coding region; coordinates of gene boundaries derived from alignment of available HRV genome sequences; gray shading of every other gene is provided for orientation in lower panels. B. Pairwise nucleotide identity scans within and between HRVA and HRVB genomes in a window of 100 nucleotides, advanced in single nucleotide steps across the genome. C. Pairwise amino acid identity scans within and between HRVA and HRVB genomes in a window of 50 amino acids, advanced in single amino acid steps across the genome. D. Ratio of the number of non-synonymous to synonymous mutations (dN/dS) across the genome inferred from the sequences of the HRVA (red plot) and HRVB (blue plot) genomes. Maximal dN/dS for window size of 3 codons, advanced in single codon step, are plotted. For panels B and C, bold plots, correspond to average % pairwise sequence identity values; pale plots, minimum and maximum % pairwise sequence identity values.