Issue with Circularization Check for Large Mitogenomes in MitoFinder

[meeranhussain]

Hi,
I have assembled the mitogenomes of 8 Microctonus aethiopoides using Flye in meta mode on ONT data. The mitogenomes were extracted from the assembly using the GetOrganelle tool. According to the Flye output info file and GetOrganelle stats, the contigs were circular. However, when I tried annotating these genomes using MitoFinder, the circularization check failed for 6 out of the 8 assemblies.

These genomes are 30-32kb in size, which is larger than typical insect mitogenomes due to higher tandem repeats in the control regions.

Do you think the increased size and tandem repeats could be causing the circularization check to fail? Additionally, is it reliable to use the annotation files despite this failure in the circularization check?

I would appreciate your insights on this issue.

Cheers,
Meeran

[RemiAllio]

Hi,

I am sorry for the late reply, I didn't see your message earlier.

Unfortunately the circularization check is not very sophisticated... The way it works is as follows:
MitoFinder blast the two ends of the contig and check whether these portions are identical or not. If so, it suggests that the two ends are indeed the same portion and, when we expect a circular genome, it means that the genome is full and can be circularized. It might not work if your mitochondrial genome is circularized but the two similar ends are very long. In that case when the blast is performed with the very beginning of the 5' and the very end of the 3', the portions compared are not the same in the mitochondrial genome... I tried to draw an example in the file attached. Let me know what you think about this!

However, it shouldn't affect the annotation. That said, I recommend always checking for any unusual annotation results. Since you have 8 mitochondrial genomes, you can quickly compare the annotations between them.

Hope this helps,
Best,
Rémi