Sequencing and assembly of mitochondrial DNA

Question

[Diego]

Hi, I have just assembled the nuclear genome of two species and I am wondering if it is possible to also assemble the mitochondrial DNA using the same DNA reads I used for the nuclear genome. Is there a ways to "rescue" mitochondrial reads from a general gDNA extraction or one needs to select mitochondrial DNA during the DNA extraction? (special DNA extraction kit for mitochondria)

Thanks in advance, Diego

Answer 1

[Corentin]

Hi,

I recently assembled chloroplast and mitochondrial genomes from total DNA, so it is definitely possible but it depends on your data and species of interest.

There are several assemblers which first extract organelle reads and then perform the assembly:

• GetOrganelle (as mentioned by ponganta https://github.com/Kinggerm/GetOrganelle)
• Novoplasty (https://github.com/ndierckx/NOVOPlasty)

Alternatively, you could manually align your reads to organelles of similar species to extract the organelle reads and use a "classic" assembler (Spades for example). But, I would suggest trying the specialised tools first.

If you are also interested in annotation after the assembly, I can suggest GeSeq: https://chlorobox.mpimp-golm.mpg.de/geseq.html

[ponganta]

+1 for novoplasty. I forgot about that one. It works really well (used it extensively on RNA-Seq data of plastidary transcripts)

Answer 2

[Jeremy Leipzig]

Mitochondria can outnumber nuclear dna by 1000x, so I don't think you need to enrich for it.

Answer 3

[ponganta]

Would getorganelle be an option? It is available via Conda.