Lawrence Berkeley National Laboratory

The chloroplast genome of Pelargonium e hortorum has been completely sequenced. It maps as a circular molecule of 217,942 bp, and is both the largest and most rearranged land plant chloroplast genome yet sequenced. It features two copies of a greatly expanded inverted repeat (IR) of 75,741 bp each, and consequently diminished single copy regions of 59,710 bp and 6,750 bp. It also contains two different associations of repeated elements that contribute about 10 percent to the overall size and account for the majority of repeats found in the genome. They represent hotspots for rearrangements and gene duplications and include a large number of pseudogenes. We propose simple models that account for the major rearrangements with a minimum of eight IR boundary changes and 12 inversions in addition to a several insertions of duplicated sequence. The major processes at work (duplication, IR expansion, and inversion) have disrupted at least one and possibly two or three transcriptional operons, and the genes involved in these disruptions form the core of the two major repeat associations. Despite the vast increase in size and complexity of the genome, the gene content is similar to that of other angiosperms, with the exceptions of a large number of pseudogenes as part of the repeat associations, the recognition of two open reading frames (ORF56 and ORF42) in the trnA intron with similarities to previously identified mitochondrial products (ACRS and pvs-trnA), the loss of accD and trnT-GGU, and in particular, the lack of a recognizably functional rpoA. One or all of three similar open reading frames may possibly encode the latter, however.