2.6 Recombination analysis
The whole-genome sequences were aligned and analyzed with a
recombination detection program (RDP version 4.22) (Martin et al., 2010)
to investigate recombinant events. The general setting algorithm
supported the recombination breakpoint detection using seven
recombination detection methods, namely RDP, GENECOV, Bootscan, MaxChi,
Chimaera, SiScan, and 3Seq, respectively. Only recombination events
identified by at least five methods with the p -values cut-off of
0.01 were accepted. Bonferroni correction was applied throughout the
analysis. Furthermore, the aligned sequences were re-analyzed with
SIMPLOT software v. 3.5 by Bootscan methods to confirm the potential
recombination sequences (Lole et al., 1999). Phylogenetic tree analysis
was reconstructed for putative recombinant data of separate regions of
the proposed parental strains.