Control Region Annotation

Question

[Schmendrick]

Hey All,

Pretty simple q here but one which I can't seem to solve....

Does anyone know of a mitochondrial genome annotator that will annotate the control region? I've used MITOS for whole mitogenome annotation but it doesn't give details on sub-regions within the CR (hypervariable regions for example). I'm using a species (wildcat) for which there are no existing annotations and the control region between this species and the domestic cat (which does have good annotated sequence data available) vary considerably.

Cheers

[natasha.sernova]

There are some results for snow leopard and other other cats/ These articles may be helpful.

Below you will see a complete mitichondrial denome of Panthera uncia:

http://snowleopardnetwork.org/bibliography/Wei_2008.pdf

The complete mitochondrial genome structure of snow leopard Panthera uncia

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138527/

Annotated features of domestic cat – Felis catus genome

The paper mentions some founded repeats in mtDNA

http://www.snowleopardconservancy.org/pdf/janeckagenetic.pdf

There are equences of seven snow leopardn Panthera uncia -specific microsatellite primers menyioned inside:

[WouterDeCoster]

Can you explain more how those papers are related to annotating the mitochondrial genome?

Answer 1

[Schmendrick]

Thanks for the replies. I should have been more clear that I'm working with subspecies Felis silvestris silvestris, the European wildcat. There are differences in Control Region length and composition within this subspecies group so its v unlikely that annotations taken from a different species will be helpful. I'm really looking to be able to annotate the Control Region directly from the sequences I've generated. I thought it'd be easy to find an annotator, seems not... :(

Cheers M

[WouterDeCoster]

So, just based on the nucleotide sequences you want to predict functional domains? I'm not sure reliable tools doing that exist.

[Schmendrick]

There are a couple of programs that are fairly good at annotating functional genes and non-coding regions from mitochondrial nucleotide sequences (MITOS is one). They just don't annotate the hypervariable (HV) regions within the non-coding control region. I know there has to be a way to do it because there are plenty of examples in the literature of authors sequencing whole mitogenomes from species with no existing reference data and they've annotated the HV regions. Unfortunately none I've read thus far details how they've done it.