ANALYSIS OF A HOTSPOT FOR DELETION FORMATION WITHIN THE INTRON OF THECHLOROPLAST TRNI GENE

The chloroplast genomes of higher plants encode several tRNA genes tha t contain highly conserved type II introns. Using primers specific to conserved 5' and 3' regions within the introns of the genes trnA (tRNA -ala) and trnI (tRNA-ile) we have PCR amplified parts of these introns from 36 plant species representing a wide range of plant families. De letions were found in the introns of both tRNA genes. Fourteen species had detectable deletions within the intron of trnI and four species w ithin the intron of trnA. The occurrence of these deletions among the various plant families suggests that the events leading to the formati on of these deletions occurred independently many times during the evo lution of higher plants. Analysis of the amplified PCR products from t he trnI intron suggests that these independent deletions may not be ra ndom but appear to fall into two size classes. Several members of each class were cloned and sequenced and the end points of the deletions w ere mapped. The 3' ends of all deletions studied terminate within the same short region. The 5' ends of the deletions map to two different r egions, giving rise to the two size classes. These two 5' deletion end point regions show some sequence similarity. Only two of the identifie d deletions contain directly repeated sequences at the deletion endpoi nts, a feature associated with homologous recombination. Our results s uggest that within the trnI intron, there are preferred sites or ''hot spots'' for deletion formation involving a novel imprecise recombinati on mechanism. The significance of these sequences and possible mechani sms for deletion formation are discussed.