The study of organelle genes and genomes is essential to our understanding of eukaryotic cellular and molecular biology. The proper functioning of organelles in all eukaryotic cells involves a precise cooperation between nuclear and organellar genetic systems. Defects in this functioning have direct consequences for human health, as is evident from the recent explosion of reports on mitochondrially inherited diseases. This proposal addresses two fundamental questions in the genetic coevolution of the eukaryotic cell: l) How are organelle genes functionally transferred to the nucleus and what are the consequences of these genetic relocations? 2) To what extent can organelle mutation rates change radically, either across the whole genome or for a specific set of genes, and what are the underlying causes and consequences of this change? First, several cases of recent gene transfer will be explored in order to l) fully develop the coxII transfer as a paradigmatic case of "gene transfer caught in the act", i.e., the elaboration of a transcompartmental gene-family that is actively sorting out gene function between the mitochondrion and the nucleus; 2) determine whether gene transfer or gene substitution events have occurred across all three genetic compartments for the ribosomal protein gene rps7; 3) determine whether chloroplast genes are transferred to the nucleus via RNA intermediates; 4) test the hypothesis that nuclear spliceosomal introns can evolve from organelle-derived group II introns; and 5) determine whether the mitochondrial genome is fundamentally dispensable or required, perhaps because it encodes two key, unimportable respiratory proteins. Second, we will accurately measure the extraordinary elevation in mutation rate of the mitochondrial genome in Pelargonium, determine whether its lack of RNA editing reflects wholesale genome retroprocessing, and investigate a possible mechanistic link between these two features. We will also document the full extent of the highly accelerated evolution that is specific to the four chloroplast genes encoding RNA polymerase, as well as search for associated changes in chloroplast promoter and RNA polymerase usage.