This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The chloroplast of the common geranium, Pelargonium hortorum, contains the largest plastid chromosome of any land plant, and has undergone numerous structural rearrangements (inversions and transpositions) and gene duplications, making this a very active and dynamic genome. Our working hypothesis was that these extensive structural alterations are due to recombination events mediated by small dispersed repeat elements scattered throughout the genome. A collaborative effort was initiated with investigators at 3 other institutions (University of Texas/Austin, University of California/Berkeley, and Indiana University) and the DOE Joint Genome Institute and Lawrence Berkeley National Laboratory to sequence and annotate the entire geranium chloroplast genome. This effort has now been completed and is being submitted for publication. All likely genes have been annotated, several gene losses have been documented, and several families of repeat elements have been identified and mapped. These repeats are located at the borders of rearranged sequences and thus seem likely to mediate recombination events that would lead to rearranged genomes. Models have been proposed that account for the major genome rearrangements and can be tested by examining related species for intermediate states. In geranium one and possibly two transcriptional operons have been disrupted, leading to a potential change in gene regulation. Despite the increase in size and complexity of the genome the gene content is similar to that of other flowering plants with the exception of a large number of pseudogenes. These findings have implications for understanding genome structural evolution and gene rearrangements in other circular genomes, such as those of human mitochondria.
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