In land plants, most plastomes display a tetrapartite genome organization with a large single copy region (LSC) and a small single copy region (SSC) separating tow inverted repeat regions (IRA and IRB; Fig. 1). The two IRs are identical in their nucleotide sequence, so that every gene contained within them is present in two copies per genome which only differ in their relative orientation (Fig. 1). The boarders between the IRs and the single copy regions are somewhat variable even between closely related species (Goulding et al. 1996). Expansion of the inverted repeat region is extreme in Pelargonium, the flowering plant species with the largest plastome (217 kb; Palmer et al. 1987; Chumley et al. 2006). Here, the IRs are 75 kb in size each and thus about three times as big as in most other higher plants. The functional significance of the presence of the IR region in two copies is not quite clear. Increasing the gene dosage of highly expressed genes (such as the ri-bosomal RNA genes; Fig. 1) and genome stabilization (Palmer and Thompson 1982) have been proposed as possible reasons why having this large inverted duplication could be beneficial. Its absence from some algal (Reith 1995) and even some higher plant plastomes (Palmer and Thompson 1982), however, indicates that the IR is not essential for plastome maintenance and/or function.
The presence of two large identical regions in the plastome facilitates two types of genetic interactions between homologous sequences: intramolecular recombination and gene conversion (Birky and Walsh 1992; Khakhlova and Bock 2006). Homologous recombination between the two IRs produces two isoforms of the plastid genome (dubbed flip-flop recombination; Palmer 1983; Stein et al. 1986), which differ in the relative orientations of LSC and SSC. Circumstantial evidence for the action of gene conversion in the IRs has come from the observation that the mutation frequency of genes in the IR regions is significantly lower than for genes located in the two single copy regions of the plastome (Wolfe et al. 1987; Maier et al. 1995). Gene conversion biased on average towards the wild type sequence has been proposed to account for the lower mutation rate in the inverted repeats (Birky and Walsh 1992). The recent experimental demonstration of high gene conversion activity in plastids (Khakhlova and Bock 2006) lends support to this hypothesis.
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