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Open Access Short report

Recombination analysis of Soybean mosaic virus sequences reveals evidence of RNA recombination between distinct pathotypes

Alla G Gagarinova124, Mohan Babu1, Martina V Strömvik3 and Aiming Wang12*

Author Affiliations

1 Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford St., London, Ontario, N5V 4T3, Canada

2 Department of Biology, The University of Western Ontario, Biological & Geological Building, 1151 Richmond St., London, Ontario, N6A 5B7, Canada

3 Department of Plant Science, McGill University, 21111 Lakeshore Rd., Ste. Anne de Bellevue, Québec, H9X 3V9, Canada

4 Department of Molecular Genetics, The University of Toronto, Toronto, M5S 1A8, Canada

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Virology Journal 2008, 5:143  doi:10.1186/1743-422X-5-143

Published: 26 November 2008

Additional files

Additional File 1:

List of full-length and partial (P1, CP) sequences of SMV analysed for recombination. A list of all sequences and the corresponding Genbank accession numbers are provided.

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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 [19] 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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Additional File 3:

Supplemental Figure 1. Similarity plots with G5 as the query isolate. Lists of isolates included in the analyses with their corresponding line colors are shown in the legend box. Locations of sites 'w', 'x', 'y', and 'z' are demarcated with vertical lines and the green underlined letters. Regions used for "find sites" analyses are marked with rectangles; names for the query, first and second parental, as well as outgroup isolates, with respective numbers of informative sites, supporting each grouping, and the χ2 values are given for each recombination site in matching colors.

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Additional File 4:

Supplemental Figure 2. Similarity plots with G7H as the query isolate. Lists of isolates included in the analyses with their corresponding line colors are shown in the legend box. Locations of sites 'w', 'x', 'y', and 'z' are demarcated with vertical lines and the green underlined letters. Regions used for "find sites" analyses are marked with rectangles; names for the query, first and second parental, as well as outgroup isolates, with respective numbers of informative sites, supporting each grouping, and the χ2 values are given for each recombination site in matching colors.

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Additional File 5:

Supplemental Figure 3. Similarity plot with G7f as the query isolate. List of isolates included in the analysis with their corresponding line colors are shown in the legend box. Location of each statistically significant recombination site is demarcated with a vertical line and a green underlined letter, adjacent to the line. Names for the query, first and second parental isolates, and outgroups with corresponding numbers of informative sites, supporting each grouping are given in red and blue, respectively. The χ2values for each recombination site are given in italicized underlined font, adjacent to the vertical line demarcating each respective recombination site.

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Additional File 6:

Supplemental Table 1. Effect of informative site nucleic acid differences on amino acid composition in analyses of G7f recombination events with remotely related non-SMV potyvirus sequence (PPV) as outgroup. Informative sites that are also found in analyses with Aa as outgroup [see Additional file 7] are given in italics.

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Additional File 7:

Supplemental Table 2. Effect of informative site nucleic acid differences on amino acid composition in analyses of G7f recombination events with Aa as outgroup. Informative sites that are also found in analyses with non-SMV potyvirus sequence (PPV) as outgroup [see Additional file 6] are given in italics.

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