Some inconsistencies do exist between bacteria and plastids/mitochondria. Mitochondria possess the ability to fuse with other mitochondria (this is believed to be the result of simplification that has occurred within the mitochondrial membranes over time) and the genetic information within a mitochondrion or plastid also differs in some ways to that of bacteria. These organelles possess higher concentrations of introns (DNA that will be spliced out prior to translation) than bacteria and intron types not found in bacteria. The genomes of these organelles are also much smaller than those of bacteria.

Gene flow between the nucleus and the organelles is believed to be responsible for the genetic discrepancies. Gene flow from the nucleus to an organelle first requires a copy of a segment of DNA from the organelle to insert into the nuclear DNA and gain expression. Loss of function can then occur in the original gene. A similar process can explain migration from the nucleus to the organelles. While organelle DNA fragments within nuclear DNA are rather common, nuclear DNA fragments within organelle DNA are rare (the exception being plant mitochondria which has experienced a rather large increase in genome size over time). Such genetic transfers operate with a frequency similar to that of mutation.

The introns within the organelles and the increase in the plant mitochondria genome over time are thought to be due to a transfer from the nucleus to the organelles. The size discrepancy between the genome sizes of chlor-oplasts and mitochondria is believed to be a result of selection for genes originally possessed by the organelles to reside in the nucleus.

Selection for the migration of genes to the nucleus comes in many possible forms. First, it is believed to be physically more difficult for DNA to enter these organelles as compared to the nucleus. Population genetics also tells us that sexual reproduction (which many eukar-yotes posses) enables the more rapid spread of advantageous genes, and overcomes Muller's ratchet (the idea that asexual reproduction lacks an effective means of ridding the genome of deleterious mutations that gradually build up). Also, chloroplasts and mitochondria perform redox (reduction-oxidation) reactions, which are prone to producing deleterious mutations. Finally, it has been proposed that smaller organelle genomes would replicate faster than those with redundant genes and thus be selected for.

The reasons for maintenance of organelle DNA are not as clear. Some reasons might include, that the remaining genes code for proteins that cannot be easily transported into the organelle (possibly membrane-spanning or strongly hydrophobic proteins) or that these genes are harmful if expressed in the cytoplasm. Another potential reason may be the slight differences in organelle versus nuclear transcription/translation.

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