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.