Fig. 1
From: Intra-species recombination among strains of the ampelovirus Grapevine leafroll-associated virus 4
Analysis of recombination events in the genome of GLRaV-4 strains. (a) Graphical representation (not drawn to scale) of the generalized genome map of GLRaV-4. Individual open reading frames (ORFs) are shown as boxes with associated protein designations used for closteroviruses [2] and numbered 1 to 6 above the diagram. Abbreviations of ORFs: L-Pro, papain-like leader protease; MET, methyltransferase domain; HEL, RNA helicase domain; AlkB, the AlkB domain; RdRp, RNA-dependent RNA polymerase; p5, 5 kDa protein; Hsp70h, heat shock protein 70 homolog; CP, coat protein; p23, 23 kDa protein. Lines at the genome extremities represent non-translated regions. b Putative recombinant events in isolates LR106 and Estellat. (B-1) and (B-2) represent, respectively, recombination event-1 (nt 4105–5240) and event-2 (nt 627–1551) in ORF1a of the LR106 isolate and (B-3) represents recombinant event (nt 1–6312) in the genome of the Estellat isolate identified by the RDP. The X-axis indicates the nucleotide position in the alignment and the Y-axis shows informative nucleotide pairwise identity between parental and recombinant isolates. The color key of the parental isolates is shown next to the plots