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â¢ Mitochondrial DNA is found inside the mitochondria while nuclear DNA is found inside the nucleus of a cell. â¢ One cell contains approximately 99.75% of nuclear DNA and 0.25% of mitochondrial DNA.â¢ The mutation rate of mitochondrial DNA is nearly twenty times faster than that of nuclear DNA.he uniqueness of mitochondrial DNA is that it is maternally inherited as a linked set of genes, passed on to progeny in the cytoplasm of the egg cell; thus no recombination between maternal and paternal genomes occurs.
â¢ In eukaryotes, DNA is found mostly in the cell nucleus, but some are in mitochondria and chloroplast while, in prokaryotes, it is found in the cytoplasm. â¢ DNA usually occurs as circular chromosomes in Prokaryotes while it is linear chromosomes in Eukaryotes.ll the animals, plants, and fungus are eukaryotic organisms; nuclear envelope is the most defining character for all eukaryotic organisms. In eukaryotes, mostly DNA is stored inside the cell nucleus, but some are found within the organelles such as chloroplasts and mitochondria.