In planta deletion of DNA inserts from the large intergenic region of cauliflower mosaic virus DNA.

RNA splicing and copy-choice recombination lead to deletions in the DNA of cauliflower mosaic virus (CaMV). To assess the relative importance of these mechanisms of nucleotide sequence change, free of constraints imposed by the "relay race" mode of translation of CaMV RNA, we examined the stability of inserts in the large intergenic region. The insertions had, in various combinations, splicing signals and directly repeated sequences that could facilitate deletion. Most modified DNAs were infectious. Viral DNA recovered from infected plants was analyzed by restriction and, in some cases, cloned for nucleotide sequencing to determine deletion endpoints. Deletions from a DNA containing introduced splicing signals occurred primarily at direct repeats, although deletion apparently by splicing was also detected. Both types of deletion were also observed with insertions containing a 5' splice donor but no known functional 3' splice acceptor. One DNA, whose insertion lacked splicing signals and short repeated sequences, was stable in one of two plants infected. Total insert deletions were bounded by repeats or pseudorepeats, while partial insert deletions apparently occurred by splicing. The results suggest that the two mechanisms for deletion of nucleotides are equally important in the evolution of caulimoviral nucleotide sequences.