Comparative studies of the structure of chloroplast DNA from four species of Oryza: cloning and physical maps

Chloroplast DNAs (ctDNAs) were prepared from the mature green leaves of three species in the genus Oryza, namely, O. punctata (genome type BB), O. offici-nalis (CC), and O. australiensis (EE). After digestion with restriction enzymes, ctDNAs were cloned into a lambda phage vector and overlapping clone banks of the entire chloroplast genome from each of the three Oryza species were obtained. BamHI and PstI restriction maps of the ctDNAs were constructed, and the structures of the ctDNAs from O. sativa and the other three Oryza species were compared. Two types of variation were noted: the gain or loss of restriction sites, and deletion or insertion of nucleotides. We detected two independent deletions in the BamHI-3/PstI-3 fragment of O. punctata and in the BamHI-5/PstI-11 fragment of O. officinalis, each of which was shorter than the respective fragment from O. sativa, and the deletions were located in spacer regions. Short direct-repeat sequences were detected at the border of both deletions, indicating that these deletions were results of intramolecular recombination mediated by these direct repeats. Further analysis on distribution of those deletions among 15 Oryza species revealed that the deletions found in this study represent genotype-specific variations.