A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred irrespective of the location or the size of the gene in the organellar genome; large genes and, in some cases the entire organellar genome, have been found in the nucleus.

Gene transfer to the nucleus is coupled with the loss of the genetic autonomy of the organelle. However, many of the proteins coded by the exported genes are still produced by the nucleus and transported back to the organelle. This is possible as the genes are modified to be compatible with nuclear transcriptional and translational machinery and undergo changes such as the addition of a promoter and a terminator. A targeting sequence is also added, so the resulting proteins get delivered to the specific organelle. This also enables the nucleus to control the supply of these proteins and regulate the biogenesis of the organelles. Sometimes, such exported genes evolve and perform new functions for the organelles other than their parent one. For example, almost 50% of plastid-derived genes in Arabidopsis thaliana carry out non-plastid functions.

There are several theories as to why organisms transfer genes from the organelles to the nucleus. Both mitochondria and chloroplasts generate free radicals which can cause harmful mutations in their DNA. Transfering vulnerable organellar genes to the nucleus may be one of the strategies to protect them from mutations. According to the genetic principle Muller’s ratchet, asexual reproduction leads to the accumulations of deleterious mutations which eventually can cause the extinction of the species. However once transferred to the sexual genome of the nucleus, the exported gene can undergo sexual recombination which helps it to prevent the accumulation of harmful mutations.