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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¢ Mitochondrial DNA may contain more than thousand copies per cell while nuclear DNA has only two copies per cell. â¢ The chromosomal paring of nuclear DNA is diploid whereas that of mitochondrial DNA is haploid. â¢ Generational recombination and replication repair is present in nuclear DNA. Unlike nuclear DNA, all mitochondrial DNA comes from the mother and none comes from the father (maternally inherited). Nuclear DNA contains more information coming from both parents (both paternal and maternal).