Fig. 2.

Veg6 ACMV and EACMCV nucleotide diversity sliding windows. (a) Sliding window analysis of nucleotide diversity (π) of ACMV DNA-A and DNA-B and (c) EACMCV DNA-A and DNA-B. Red to pink represents the nucleotide diversity across the genome of inoculated plants (p1) and two vegetative propagations (p4 and p6). Enhanced views of the nucleotide diversity of the AV1 and AC1 open reading frames during P1, P4, and P7 for ACMV-A (b) and EACMCV-A (d). Blue lines mark the locations of codons encoding functional motifs in the Rep protein, i.e. Rep C, Rep B, Walker B, Walker A [63], Motif 3 [62], GRS [64], Motif 2 [62] and Motif 1 [83]. The motifs are shown to scale. Genome coordinates (nt), the positions of open reading frames and their directions of transcription are shown below each graph.