2.7 Recombination analysis
In order to analyze the potential recombinant evidence, an integrated
software package for 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 were identified by at least
three of the aforementioned methods, and the p -value <
0.05 were considered plausible recombinant events. The sequences in the
analyzed 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 which had
contributed to the detected recombinants (with the major parent
contributing the larger fragment and the minor parent the smaller).