Which mitochondrial genomes in RefSeq are complete?

Question

[Cytosine]

This one has me puzzled...

I'm trying to compare mitochondrial genomes and I'm looking for the complete and finalized versions from genbank only.

So far, I've thought that the RefSeq database would be the place to look in, but I've stumbled across 2 entries that got me thinking. (both of them are in the RefSeq database)

One of them starts with the accession - NC_ and is followed by the suffix mitochondrion, complete genome

The other one starts with the accession - NW_ and is followed by mitochondrial scaffold, whole genome shotgun sequence

I'm surprised here because I thought that WGS entries are not yet entered into RefSeq, until final curation (which I'm guessing is not gonna happen, since this is an entry over 5 years old).

The latter scaffold seems to contain the full mitochondrial genome, judging from sizes of mitochondria of related species, and it is also more or less annotated.

Is such a (non-finalized?) WGS mitochondrial genome reliable enough to be used in comparisons? What arguments can be used for and against it?

Answer 1

[5heikki]

This is a really handy resource for organelle genomes.

[Cytosine]

Thank you, but I'm already using that one, which is a RefSeq subset of mitochondrial genomes.

However, it also contains the same entries which are in the WGS section and made me post the original question.

Answer 2

[Jeremy Leipzig]

rCRS is NC_012920

For all full-length MT sequences you can use this handy search query from MITOMAP:

http://www.ncbi.nlm.nih.gov/nuccore/?term=(015400[SLEN]:016600[SLEN])+AND+Homo[Organism]+AND+mitochondrion[FILT]+NOT+(Homo+sp.+Altai+OR+Denisova+hominin+OR+neanderthalensis+OR+heidelbergensis+OR+consensus+OR+ancient+human+remains)