I want to extract mitochondrial DNA from a fungus, but there are two ways to cultivate the fungus, one is to cultivate it on an agar medium (covering a piece of cellophane paper to stop hyphae to grow into the medium) in a petri dish, and the other is to cultivate it in a liquid medium in an erlenmeyer flask (shaking during cultivation). Do you know, between the two ways, which is better for getting high yeilds of mitochondrion and mitochodnrial DNA?
I ask because I ever used the first way to cultivate and performed RNA-seq, but the number of mitochondrial reads only accounted for 0.05% of total reads. I expect at least 0.5%. So, I'm not sure if the second way of cultivation would help me.
Any comments are appreciated.