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.