The gene coxII, normally present in the mitochondrion, was functionally transferred to the nucleus during flowering plant evolution. coxII transfer is estimated to have occurred between 60 and 200 million years ago, whereas loss of coxII from the mitochondrion occurred much more recently, being restricted to a single genus of legumes. Most legumes have coxII in both the nucleus and the mitochondrion; however, no evidence is found for simultaneous coxII expression in both compartments. The nuclear coxII sequence more closely resembles edited mitochondrial coxII transcripts than the genes encoding these RNAs. Hence, gene transfer appears to have involved reverse transcription of an edited RNA intermediate. The nuclear gene contains an intron at the junction of the transit peptide sequence and the mature protein-coding sequence; exon shuffling may have played a role in assembling a functional coxII gene in the nucleus.

The respiratory gene cox2, normally present in the mitochondrion, was previously shown to have been functionally transferred to the nucleus during flowering plant evolution, possibly during the diversification of legumes. To search for novel intermediate stages in the process of intracellular gene transfer and to assess the evolutionary timing and frequency of cox2 transfer, activation, and inactivation, we examined nuclear and mitochondrial (mt) cox2 presence and expression in over 25 legume genera and mt cox2 presence in 392 genera. Transfer and activation of cox2 appear to have occurred during recent legume evolution, more recently than previously inferred. Many intermediate stages of the gene transfer process are represented by cox2 genes in the studied legumes. Nine legumes contain intact copies of both nuclear and mt cox2, although transcripts could not be detected for some of these genes. Both cox2 genes are transcribed in seven legumes that are phylogenetically interspersed with species displaying only nuclear or mt cox2 expression. Inactivation of cox2 in each genome has taken place multiple times and in a variety of ways, including loss of detectable transcripts or transcript editing and partial to complete gene loss. Phylogenetic evidence shows about the same number (3-5) of separate inactivations of nuclear and mt cox2, suggesting that there is no selective advantage for a mt vs. nuclear location of cox2 in plants. The current distribution of cox2 presence and expression between the nucleus and mitochondrion in the studied legumes is probably the result of chance mutations silencing either cox2 gene. Most of these recent evolutionary transfers involve mt genes in plants (e.g., refs. 3-9); in contrast, the numerous sequenced mt genomes of animals all contain the same set of 13 (or occasionally 12) protein genes (10).Previously characterized cases of gene transfer have revealed several intermediate stages in the process of intracellular gene transfer. In most cases, physical transfer of plant mt genes has been inferred to occur by an RNA intermediate because the nuclear copy resembles an edited mt mRNA rather than an unedited mt gene (e.g., refs. 3-5). Acquisition of regulatory elements and a mt targeting sequence is critical for nuclear gene activation. This has been inferred to have occurred by recombination with a duplicated targeting sequence from a preexisting nuclear gene encoding a mt protein (6), by alternative splicing of a targeting sequence shared with a preexisting mitochondrialtargeted gene (8, 9), and by exon shuffling from a nuclear gene encoding a cytosolic protein and gain of mt targeting function (11). After nuclear gene activation, both the nuclear and mt copies should be expressed, at least transiently, but no such examples have been reported previously in plants. Inactivation (silencing) and loss have been reported only for the organellar copy but not the nuclear copy, suggesting that inactivation of the organellar gene is favored.The respiratory gene cox2, encoding subunit 2 of cy...

Physical and gene mapping studies reveal that chloroplast DNA from geranium (Pelargonium hortorum) has sustained a number of extensive duplications and inversions, resulting in a genome arrangement radically unlike that of other plants. At 217 kilobases in size, the circular chromosome is about 50% larger than the typical land plant chloroplast genome and is by far the largest described to date, to our knowledge. Most of this extra size can be accounted for by a 76-kilobase inverted duplication, three times larger than the normal chloroplast DNA inverted repeat. This tripling has occurred primarily by spreading of the inverted repeat into regions that are single copy in all other chloroplast genomes.