Downloading all eucaryote mitochondrial genomes

Question

[Eric Normandeau]

I would like to download all the complete sequences of the mitochondrial genomes available for eucaryotes. I thought that would be straight forward, and it probably is, but a GenBank search in Nucleotide using mitochondrion, complete genome for the search terms returns 43720 hits, most of which are not mitochondrion genomes.

Are there mitochondrion specific databases or a better approach to find these mitochondrion sequences?

[Sishuo Wang]

Hi Eric,

Give this link a try! It is curated by NCBI RefSeq.

Answer 1

[Neilfws]

I tried searching the NCBI Genome database with the term txid2759[Organism:exp] (eucaryotes). At the top of the results page is a link "See also 4407 organelle- and plasmid-only records matching your search". I guess many of those are mitochondria (some will be chloroplast); not sure of the next step best filter for mitochondria-only.

[Eric Normandeau]

Thank you Neil, I'll investigate in this direction.

Answer 2

[fernie.penaloza]

Hi!

You can use their "genomes" site.

http://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?opt=organelle&taxid=2759

At the right you can download a list of the accession IDs, by now there are ~5065.