I'm interested in doing de-novo sequencing but also phylogenetic analysis. In particular, after de-novo sequencing and annotating the genome, I need to align the CO1 gene and the nuclear 28S rRNA gene of several species. When extracting DNA and sequencing with PacBio for example, how does the assembler know what corresponds to nuclear and what to mitochondrial DNA?
According to this pdf, from pacb.com
isolation with mitoISO MITOISO
The kit will include three steps: 1) mechanical rupturing of tissues or cells 2) removing cellular debris and nuclei by low speed centrifugation and 3) harvesting mitochondria by high speed centrifugation.
Then, you can follow the DNA extraction with mitochondrial DNA, and then sequenced on the PacBio Sequel.
If you are doing whole genome sequencing, the mitogenome will have a higher read depth according to this article stating that lower read depth of the nuclear genome separating the two different origins:
those of mitochondrial origin & those of nuclear origin