2.5 Sequence alignment and phylogenetic analyses
Genomic sequences of two 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. The
genomic sequences of two PBoV strains and 35 reference strains (Table 2)
were aligned and analyzed 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 in the two complete
genomes of PBoV. 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.