We always asked the questions why Mitochondria retains those few genes i.e. 37 in comparison to the 20,000-plus genes in nucleus including the ones that help the mitochondria function? Moreover; why Mitochondria stayed independent by holding on to few vital genes though it may be easier and safer for the cell to maneuver all genes in the nucleus?

The recent paper in Cell Systems Johnston and Williams analyzed all the mitochondrial data across the species. Their study revealed genes that are retained in the mitochondria are related to building the organelle's internal structure and capable of dealing with the byproducts i.e. free radicals generated in the power production process (in form of ATP). Also mitochondrial proteins that are hydrophobic, or water-repelling, are more likely to be made there than elsewhere in the cell, where they might get stuck during transit through the cell's membranes.

This a good read if you want your answer: why we still have mitochondrial DNA?

Reference: Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention. Volume 2, Issue 2, 24 February 2016, Pages 101–111.