Phylogenetic and genomic recombination analysis
Multiple sequence alignments were generated using ClustalW in Lasergene
(Version 7.1, DNASTAR Inc., Madison, WI, USA). Phylogenetic trees based
on the whole genome were constructed in MEGA 6.0 using the
neighbor-joining method with 1000 bootstrap replicates. Recombination
analysis used RDP4 software with seven different algorithms (RDP,
GeneConv, BootScan, MaxChi, Chimera, SiScan, and 3Seq) and SimPlot
(version 3.5.1) by advancing a 500-bp sliding window along the genome
alignments with a 20-bp step size.