The eukaryotic cells, differently from prokaryotic cells, contain two genomes.
Mitochondrion history starts with the endosymbiotic events dated 1,5 billion years ago, when oxygen filled the atmosphere and a proto-bacterium fused with a pre-eukaryotic cell. After the endosymbiotic event, the original bacterial DNA that subsequently evolved in mitochondrial DNA, lost fragments that reached the nucleus and became inserted thereof in a more or less random fashion.
Nowadays the scenario is the following: the mitochondrion still contains a polyploidy genome but this holds only a very low number of coding for protein genes (13 is the mammalian number). However, the number of proteins necessary to fulfil the mitochondrial functions is approximately 1000 and these are ad hoc produced by the nuclear genome and thereby imported in the organelle.
Another point to take into account is the fact that mitochondrial protein synthesis is based on a genetic code that deviates from the so defined “universal code”.
These funky aspects of mitochondrial DNA raise the question why mitochondrial DNA still exists and why mitochondrion persists along the time to keep a genome although small. And in addition, what’s about the different mitochondrial genetic code? Why is it different? And from where originates?
Finally, since the nuclear genome is highly populated with DNA fragments showing high similarity with the mitochondrial DNA counterpart (NumtS - Nuclear mt sequences), the issue of whether the migration of mitochondrial DNA to nuclear DNA started already at the time of the endosymbiotic event or appeared later in the course of evolution is still debated.