Unable to find mitochondrial genes in latest rat genome(GRCr8)

Question

[dxj294]

Hello Everyone,

I am kinda stuck right now.

I recently found out that latest rat genome(GRCr8) is available for quite a while. I plan to use it and have a single cell experiment.

I aligned my fastqs to the genome and loaded into seurat object. But I am unable to find mitochondrial genes while doing QC. I have 26k total genes in my object.

I tried looking for patters like "MT-", "mt-", "Mt-" but still couldn't.

Tried to look for gene names like ND5, COX2, ATP6 in the rownames of the object, still couldn't find. I then searched on google and found none of the Mitochondrial genes are present in the latest genome.

I need to calculate the mitochondrial genes percentage in my cells to proceed with the QC. Earlier I was able to see these genes when I was using mRatBN7.2 genome

Any idea whats going on or what should I do next?

Answer 1

[GenoMax]

It appears that the mitochondrial genome has not made it to the RefSeq version of GRCr8. It is present in GenBank version though: https://www.ncbi.nlm.nih.gov/search/all/?term=CM070413.1

You could either add it to the RefSeq version (GCF_036323735.1) or use the GenBank version instead (GCA_036323735.1).

[dxj294]

Thanks for pointing it out. I appreciate the help.