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We used the chloroplast gene rbcL as a model to study the frequency and relative timing of transfer of chloroplast sequences to the mitochondrial genome. Southern blot survey of 20 mitochondrial DNAs confirmed three previously reported groups of plants containing rbcL in their mitochondrion, while PCR studies identified a new mitochondrial rbcL. Published and newly determined mitochondrial and chloroplast rbcL sequences were used to reconstruct rbcL phylogeny. The results imply five or six separate interorganellar transfers of rbcL among the angiosperms examined, and hundreds of successful transfers across all flowering plants. By taxonomic criteria, the crucifer transfer is the most ancient, two separate transfers within the grass family are of intermediate ancestry, and the morning-glory transfer is most recent. All five mitochondrial copies of rbcL examined exhibit insertion and/or deletion events that disrupt the reading frame (three are grossly truncated); and all are elevated in the proportion of nonsynonymous substitutions, providing clear evidence that these sequences are pseudogenes.

Two basal lineages of flowering plants possess an intergenic inversion in the chloroplast inverted repeat (IR), a region of the genome from which there have been few previous reports of this class of structural mutation. The size of the inversion (approximately 200 bp) places it in a class not previously seen in the plastid genome. The two lineages with the rearrangement, representatives of the orders Laurales and Nymphaeales, are not closely related and the inversion therefore probably arose independently in each group. The inversion is bordered by short, but highly conserved, inverted repeat motifs that were most likely associated with the inversion process. A stem-loop structure that involves these motifs may play a functional role in mRNA stability. It is seen in all optimal or nearly optimal predicted RNA foldings of the intergenic region.