Additional File 2.
Summary of unique recombination events identified by the Recombination Detection Program v.3.31 (RDP3). Our RDP3 automated analyses using RDP, GENECONV, Bootscan, MaxChi, Chimera, and SiScan methods  identified many highly significant recombination signals in full-length, P1, and CP alignments [please see Additional file 1 for the list of accession numbers for all analyzed sequences]. However, when two (parental) sequences are joined to form a recombinant (daughter) sequence, recombination signals will be detected in all descendants of the parental and daughter isolates as well as related sequences, provided the recombination signals have not been obscured by subsequent recombination events or strong selection. All detected recombination signals were automatically combined by RDP3 into sets of unique recombination events. The final set of the unique recombination events depended on the order in which the sequences were analyzed. This effect of sequence analysis order on the generated set of unique recombination events was particularly strong for the full-length sequences, where a large number of ancestral and overlapping recombination signals were found. This ambiguity was likely increased by the lack of full-length genome sequences representing many of the SMV strains. Manual investigation of the RDP3 results did not suggest that any one set of the unique recombination events was better than another: the complex similarity patterns between SMV sequences could arise through recombination in a number of ways (data not shown). Therefore, in accordance with the parsimony principle, we presented the output that explains the relationships between SMV isolates by the smallest number of recombination events. The largest number of unique recombination events was consistently detected by RDP3 in full-length sequences despite the fact that the smallest number of these sequences was analyzed. This may have to do with the fact that complete evolutionary history is preserved in full-length sequences, but not the partial sequences such as P1 and CP that were also analyzed here. More full-length SMV sequences must be obtained in order to describe the broad picture of how recombination affected evolution of SMV. Obtaining additional sequences will also aid in resolving uncertainties about parental and daughter isolate identities and narrowing down the locations of undetermined break points (recombination sites).
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Gagarinova et al. Virology Journal 2008 5:143 doi:10.1186/1743-422X-5-143