HAIRPINS CREATE MINUTE INVERSIONS IN NONCODING REGIONS OF CHLOROPLASTDNA

Minute inversions (4 bp in length), associated with probable hairpin s econdary structures, were inferred from comparative analysis of rp116 intron sequences from the chloroplast genomes of Chusquea species and related bamboos (Poaceae). The inverted sequences, which appear to hav e arisen independently on several occasions, comprise entire loops of the putative hairpins. The process of inversion seems dependent upon t he stem length of the hairpin and its estimated free energy of formati on. A similar inversion was uncovered for other plants in a previously published data set for a different non-coding region of the chloropla st genome, suggesting that the inversional process may be a common fea ture of non-coding DNA evolution. Several implications for phylogeneti c analysis are noted.