2.5 Sequence alignment and phylogenetic analyses
Genomic sequences of PBoV strains obtained in this study were screened
for sequence similarities using BLAST
(http://www.ncbi.nlm.nig.gov/BLAST) against the database in GenBank, and
aligned altogether with 35 reference strains (Table 2) using the
MegAlign program of the DNAstar software (version 7.1, DNASTAR Inc.,
USA). Phylogenetic analysis was performed using the minimum-evolution
method in the Molecular Evolutionary Genetics Analysis (MEGA) software
(version 6.0) with Kimura distances, and a bootstrap of 1,000
replicates.
Seven recombination detection methods (RDP, GENECONV, BOOTSCAN, MaxChi,
Chimaera, SiScan and 3Seq) embedded in Recombination detection program
(RDP 4.39) were used to detected recombinant events. Only those
recombination events supported by more than four programs were deemed to
avoid dependence on a single detection method as described previously
(Zhai et al., 2010), and the window size
was set to 20 bp, the highest acceptable P value was 0.01.