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).