Fig. 4

Genome sequence variation between PVS-H00 and PVS-H95. a Percentage analysis of transitions (Ti) and transversions (Tv). Percentage of Ti and Tv in each 200-nucleotides (nt) window are shown with light gray bar and dark gray bar, respectively, below the PVS genome map (top diagram). Gray rectangles indicate open reading frames (ORFs), and black ovals represent functional domains in replicase encoded by ORF1. MTR, methyltransferase domain; O-PRO, OTU-like protease region; P-PRO, papain-like cysteine protease region; HEL, helicase domain; POL, RNA-dependent RNA polymease domain. b Sliding window analysis of the ratio of nonsynonymous to synonymous nucleotide substitution rates (Ka/Ks) using KaKs_Calculator 2.0. To calculate the Ka/Ks ratio, the full-length genome sequence of PVS (top diagram) was modified to encode a polyprotein created by the seamless connection of six ORFs, i.e. by excluding non-translated and intergenic regions, and duplicating nucleotide sequence of the overlapping region between ORFs (middle diagram). A sliding window profile of Ka/Ks ratio in the modified genome sequences of PVS-H00 and PVS-H95 is shown with a solid line (bottom diagram). Each point plotted represents the Ka/Ks ratio within a sliding window of 75 bp with a step size of 12 bp along the sequence alignment. Ka/Ks ~ 1 (broken line) indicates neutral (i.e. no) selection, > 1 implies positive selection, and < 1 implies negative selection