2.7 Recombination analysis
In order to analyze the potential recombinant strains, an integrated software package, the recombination detection program RDP4 (Martin et al., 2010), was used to detect potential recombinant strains, parental strains, and possible recombination breakpoints. Seven methods (RDP, GeneConv, BootScan, MaxChi, Chimaera, SiScan, and 3Seq) were implemented using the RDP4 program. Recombination events that were detected by at least three of the aforementioned methods with significantp -values (<0.05) were considered plausible recombinant events. Sequences in the analysed dataset that most closely resembled the parental sequences of recombinants were defined as either “minor parents” or “major parents” based on the size of the genome fragments that these sequences had contributed to the detected recombinants (with the major parent contributing the larger fragment and the minor parent the smaller).