Mis-assembly of mitochondrial genome?

[lyy005]

Hi there,
Thank you for developing MITObim. I have a quick question about potential misassembly during the process.

I have used MITObim to assemble an insect mitogenome (target species) using another species (reference species) from the same family as the reference. MITObim took 7 iterations, with 41254 reads in the readpool. However, the resulting mitochondrial genome is not that similar to the target species. We compared the COX1 gene of the mitogenome to the COX1 gene online. The COX1 gene nucleotide similarity between the MITObim mitogenome and the target species is 86.65%, while the COX1 gene similarity between MITObim mitogenome and the reference species was 94.39%. So seems like the assembled mitogenome is actually more closely related to the reference rather than the target species.

The command I used was:
MITObim.pl -start 1 -end 30 -sample testpool -ref mt_genome -readpool 2gb.fastq.gz --quick reference.fasta

In general, I just wanted to say that MITObim did a great job. I assembled the mitogenomes of more than 10 insect species. And they all look great. Just this one species was kind of odd. And I was curious to hear about your opinions on this.

Thank you for any suggestions!

Yiyuan