Figure 1. Genome organization of PRV Kaplan and comparison of sequence conservation with strains Becker and Bartha.

A) Open reading frames (ORFs) are plotted spatially along the genome, along with their untranslated regions (UTRs). The genome proceeds from the Unique Long (UL) region into the Unique Short (US) region, with US being flanked by long inverted repeats (IR, TR). The large-latency transcript (LLT) is not translated. A horizontal bar connects the spliced portions of the UL15 ORF; splicing in the 5′ UTR of US1 is not shown for space reasons. B) Graph depicts DNA sequence conservation between PRV Kaplan and PRV Becker or PRV Bartha. Conservation is calculated from a multiple sequence alignment, and the conservation score between any two genomes is plotted from a sliding 100 bp window. C) Short sequence repeats (SSRs) are plotted as they occur along the PRV Kaplan genome. SSRs include minisatellites (repeat unit ≥10 bp), microsatellites (repeat unit <10 bp), and homopolymers (minimum length 6). D) A phylogenetic tree based on a whole-genome multiple sequence alignment demonstrates the closer relationship of PRV strains Kaplan and Bartha. Bootstrap values are shown at branch points (see Methods for details). The same result was obtained using nucleotide sequences of gC (data not shown), as was done for several recent PRV phylogenetic comparisons [33], [34], [177].