What Is The Best Way To Detect Mitochondrial/Chloroplast Genomes From Assembled Scaffolds (Whole Genome)?

Question

[arnstrm]

Hi everybody,

I am trying to figure out the best way to fish for the organelle genomes from the assembled scaffolds. I know I can align/blast organelle genome from closely related species, but not sure if this is the best way to do it. Should I use the original fastq files to do a reference based assembly (using closely related organelle genome)? Are there any program that can help me assemble just the organelle genome? Any help will be greatly appreciated! Thanks very much.

Answer 1

[Prakki Rama]

In my opinion, to detect if the scaffold is from a particular organelle say mitochondria or chloroplast, you should have either sequenced from the individual organs or organelles and assembled it. At this stage, using any assembler (either Kmer or overlapping depending on your read length) should be good enough to assemble the organelle genome.

But, If the organs are pooled and the data is assembled, then the best way would be comparing with existing organ reference genome or have a set of transcripts say all the mitochondrial genes (or proteins) and see if all of them are present in the same scaffold you assembled.

Answer 2

[predeus]

There's a quite widely used tool named MITObim.

I know it's an old question, but it keeps popping up in the search, so I figured I'll update it.