Viral isolates. We used the plasmid pCa37, which is the complete genome of the CaMV isolate Cabb-S, cloned into the pBR322 plasmid at the unique SalI restriction site [44] . To analyze recombination in different regions of the genome, we introduced four genetic markers: a, b, c, and d, at the positions 881, 3,539, 5,365, and 6,943, respectively, thus approximately at four cardinal points of the CaMV circular double-stranded DNA of 8,024 bp ( Figure 1 ). All markers, each corresponding to a single nucleotide change, were introduced by PCR-directed mutagenesis in pCa37, and resulted in the duplication of previously unique restriction sites BsiWI, PstI, MluI, and SacI in a plasmid designated pMark-S. Because, in this study, we targeted the possible exchange of genes between viral genomes, all markers a, b, c, and d were introduced within coding regions corresponding to open reading frames I, IV, V, and VI, respectively. Another important concern was to quantify recombination in the absence of selection, i.e., to create neutral markers. Consequently all markers consist of synonymous mutations (see below).