Recombination in full-length SMV sequences. A. Phylogenetic relationships of SMV isolates to each other and to PPV as an outgroup. Phylogenetic tree was constructed using full-length nucleotide sequences of isolates L [GenBank: EU871724], L-RB [GenBank: EU871725], G2 [GenBank: S42280.1], N [GenBank: D00507.2], Aa [GenBank: AB100442.1], Aa15-M2 [GenBank: AB100443.1], G5 [GenBank: AY294044.1], G7H [GenBank: AY294045.1], G7d [GenBank: AY216987.1], G7 referred as G7x [GenBank: AY216010.1], and G7 referred as G7f [GenBank: AF241739.1], CN18 [GenBank: AJ619757], HH5 [GenBank: AJ310200], HZ [GenBank: AJ312439], as well as PPV [GenBank: M92280.1], as the outgroup, and the Neighbour Joining function of ClustalX . Topologies of the Bayesian  as well as the1000 times bootstrapped least squares  and maximum likelihood  phylogenetic trees were same (data not shown). Bootstrap values for the Neighbour Joining and the maximum likelihood phylogenetic trees, out of 1000 replicates, are given at the nodes before and after the slanted line, respectively. For presentation purposes, the line marked with a star was shortened from 0.35145 to 0.04145. Automated RDP3 recombination analysis identified recombination events in all SMV isolates [please also see Additional file 1]. Filled circles demarcate likely times, when in evolution of SMV manually verified recombination events took place, while empty circles demarcate significant (P-value < 0.05) recombination events where the likely recombinant isolates were determined to be too far diverged from all available SMV sequences for the χ2 analysis of recombination and thus recombination analyses results were considered inconclusive. B. Locations of unique recombination events identified by RDP3, in relation to the full-length sequence alignment [please also see the Additional file 1]. Each full-length genome is represented by a long black bar and the corresponding underlined isolate name, given to the left of the bar. The figure shows a total of 17 unique recombination events, demarcated by the bars below the genomes the recombinant fragments have been integrated into. When an ancestral unique recombination event can be found in more than one daughter sequence, the recombination event is displayed with all corresponding daughter sequences. Locations of the unique recombination events identified by RDP, corresponding to the manually verified recombination sites, are shown with grey bars [please also see Additional file 1].
Gagarinova et al. Virology Journal 2008 5:143 doi:10.1186/1743-422X-5-143