Evolutionary re-organisation of a large operon in adzuki bean chloroplast DNA caused by inverted repeat movement

We have sequenced two sections of chloroplast DNA from adzuki bean (Vigna angularis), containing the junctions between the inverted repeat (IR) and large single copy (LSC) regions of the genome. The gene order at both junctions is different from that described for other members of the legume family, such as Lotus japonicus and soybean. These differences have been attributed to in apparent 78-kb inversion that spans nearly the entire LSC region and which is present in adzuki and its close relative, the common bean. This 78-kb rearrangement broke the large S10 operon of ribosomal proteins into two smaller operons, one at each end of the LSC, without affecting the gene content of the genome. It disrupted the physical and transcriptional relationship between the six-gene rpl23-rpl14 cluster and the four-gene rps8-rpoA cluster that is conserved in most land plants. Analysis of the endpoints of the rearrangement indicates that it probably occurred by means of a two-step process of expansion and contraction of the IR and not by a 78-kb inversion.