Amplification and alignment of the divergent nucleotide sequences. (A) Amplification of a single amplicon (1074 bp) corresponding to the partial RdRp, IR, and CP regions of isolates PO1, PL3, and CV2. NI, non-infected plant; M, λ-DNA digested with Pst I. (B) Alignment of isolates PO1, PL3, and CV2 with a CLRDV isolate from each of the Brazilian regions analyzed in this work. Black boxes represent residues present in all viruses in the alignment. Columns in the alignment with < 100% but > 60% conservation are shaded in gray. The arrow represents the break point indicated in the GARD analysis (see Figure 6). Sequences inside the black boxes are associated with subgenomic RNA formation .