Evidence for replication slippage in the evolution of Oenothera chloroplast DNA

Evolutionary relationships of four plastid genomes (plastomes) from different Oenothera species have been assessed by sequence comparisons of two intergenic regions that separate the ribosomal protein genes rpl16, rpl14, and rps8. Sequence changes include base substitutions, the occurrence of a 29-base tandem duplication, and variation in the length of two poly-A stretches. Additions/deletions in chloroplast DNA may not be useful for evolutionary comparisons more distant than these, particularly if the sequences undergo divergence after the initial event, but the length mutations reported here allow a finer resolution of the phylogeny of the closely related Oenothera plastomes than would have been possible if only base substitutions had been considered. Comparisons with the orthogous sequence from tobacco chloroplast DNA indicate the direction of change at most of the sites. The results suggest that plastomes I and II are closely related to each other, as are plastomes III and IV. Replication slippage is proposed as a mechanism to explain the length mutations.