I'm confused by mitochondrial rDNA and nuclear rDNA. Are they the same thing? If not, how different are they DNA sequence wise? Is there ITS region in mitochondrial rDNA?
Mitochondria have their own rDNA (that looks similar to bacterial rDNA) since the modern mitochondria organelles are descended from an ancestral bacteria. While the majority of proteins in mitochondria are now coded in nuclear DNA, a handful are still made inside mitochondria. That's why the mitochondrial genome also codes for transfer RNAs.