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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.
1 Mitochondrial DNA is inherited from mother only while nuclear DNA from the parents. 2  Nuclear DNA is diploid and mt-DNA is in a state of ploidy. 3  In nuclear DNA the genes are arranged in the process of recombination.his chromosome is much shorter and codes for proteins that are used in metabolic purposes. Another main difference is that mitochondrial DNA is only transmitted from mother and never from the father while nuclear DNA is inherited from both, mother and father.