MOESM2 of Intra-species recombination among strains of the ampelovirus Grapevine leafroll-associated virus 4

Additional file 2: Figure S1. Identification of putative recombination events in GLRaV-4 strains. Graphical representation of (A) the generalized genome map of GLRaV-4 (see description of open reading frames in Fig. 1A) and (B) SimPlot graphs showing nucleotide similarity across the genome of different strains of GLRaV-4. The GLRaV-4 (B1) strain 4 isolate WAMR-4, (B2) strain 5 isolate WASB-5 and (B3) strain 6 isolate Estellat were used as query sequences in respective plots. The X-axis indicates nucleotide position in the alignment and the Y-axis shows percent nucleotide similarity. GenBank accessions of GLRaV-4 used in this analysis were strain 4 isolate LR106 (FJ467503.1), strain 5 isolate 3138–03 (JX559639.1), strain 5 isolate TRAJ1-BR (KX828702.1), strain 6 isolate Estellat (FJ467504.1), strain 9 isolate Man086 (KJ810572.1), strain Pr (AM182328.4) and strain Car (FJ907331.1). Strain Ob (KP313764.1) and strain 5 isolate Y217 from New York (FR822696.2) were not included in the analysis due to the lack of sequence at the 5′ terminus. The color key of the isolates is shown next to the plots.