Proliferation of direct repeats near the Oenothera chloroplast DNA origin of replication

The spacer between the 16S and 23S rRNA genes of the chloroplast DNA hasbeen implicated as an origin of replication in several species of plants.In the evening primrose, Oenothera, this site was found to vary greatly insize, with plastid genomes (plastomes) being readily distinguished. Todetermine whether plastome "strength" in transmission could be correlatedwith variation at oriB, the 16S rRNA-trnI spacer was sequenced from fiveplastomes. The size variation was found to be due to differentialamplification (and deletion) of combinations of sequences belonging toseven families of direct repeats. From these comparisons, one short seriesof direct repeats and one region capable of forming a hairpin structurewere identified as candidates for the factor that could be responsible forthe differences between strong and weak plastome types. Ample sequencevariation allowed phylogenetic inferences to be made about therelationships among the plastomes. Phylogenetic trees also could beconstructed for most of the families of direct repeats. The amplificationsand deletions of repeats that account for the size variation at oriB areproposed to have occurred through extensive replication slippage at thissite.