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Figure 4 | Virology Journal

Figure 4

From: A highly divergent South African geminivirus species illuminates the ancient evolutionary history of this family

Figure 4

Pairwise genome scans of local nucleotide sequence similarities (uncorrected by any evolutionary model – corresponding to p-distances in MEGA 4.0 with pairwise deletion of gaps) within a moving 100 nucleotide window between ECSV (isolate ECSV [Za-Gre3-g257-2007]), BCTIV and representatives of the four established geminivirus genera. Each coloured plot represents a different pairwise nucleotide sequence alignment (using CLUSTAL W with a gap open penalty of 6 and gap extension penalty of 3) between a single representative of each of the six main geminivirus lineages and representatives of all the other lineages. The grey plots represent analogous scans between 20 geminivirus genome pairs in which the positions of nucleotides have been randomly reshuffled and aligned using the same settings used to align the unshuffled nucleotide sequences. The maximum and minimum bounds of these scans represent the degrees of sequence similarity expected following alignment amongst unrelated sequences with the same nucleotide composition as the real geminivirus sequences.

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