Fig. 3

Recombination analysis using Simplot 3.5.1 and RDP 3.4.1. a. Similarity plot analysis of full genome sequences of strain ZW, B, SYG61v, YZ99–6, and YY using Simplot. Bootscan analysis was executed with the following parameters: 1000 bootstrap replicates, sliding window of 200 bp, and step size of 20 bp. Strain ZW was used as query. b. Recombinant events that occurred in strain ZW were detected by RDP. The first recombination breakpoint began at nucleotide position 424 and ended at nt position 615. The second recombination breakpoint began at nucleotide position 3120 and ended at nt position 4246. In these recombinant events, strain YY is the major parent. SYG61v is the sole minor parent in the first recombinant site