A B C Qab C Qa B C Qa B C

Fig. 2. a) Tandemly repeated linear DNA sequences, b) Circularly permuted linear DNA sequences of fixed length, and c) Multimeric linear DNA molecules of variable sizes and a number of dispersed ends will give rise to d) Circular sequence maps. Arrows indicate orientation of sequences. Molecules starting with the letters c or d are not shown in c).

was mainly comprised of sub-genomic linear DNA forms, which could represent breakage products of circular plastid DNA molecules or even contaminating nuclear DNA (Fig. 3a). Breakage during extraction would give rise to variable ratios of circles to linear products with each preparation. In a later study, three to four percent of circular species were found to be dimers (Kolodner and Tewari 1979). These were arranged head-to-tail in P. sativum chloroplasts, and both head-to-head and head-to-tail in S. oleracea and Lactuca sativa chloroplasts. The majority of L. sativa and S. oleracea chloroplast DNA dimers (about 80%) were arranged head-to-head (Kolodner and Tewari 1979; see also Section 8 and Fig. 8a). In an independent study on S. olereacea and other dicots 80% of chloroplast DNA molecules were found as monomer circles and 10 to 15% as dimers. About 15% of circles were supercoiled (Herrmann et al. 1975).

An elegant more recent study utilised fluorescence in situ hybridization (FISH) involving extended DNA fibres and plastid DNA probes (Lilly et al. 2001). At the time of writing this single report remains the only published source for FISH-based analysis of plastid DNA in flowering plants. Purified chloroplasts were lysed and DNA fixed directly on a slide before hybridization providing less opportunity for DNA breakage. Using this method, chloroplast DNA from A. thaliana and N. tabacum was found to be comprised of a multimeric series of circular and linear DNA molecules (Fig. 3b). Circles comprised about 40-50% and linear DNA species about 20-25% of chloroplast DNA molecules. The remaining molecules

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