Best practice when talking about a genome

Question

[Juke34]

Hello,

I'm wondering what people usually think behind the term "genome" ? Is it only the ""nucleome"", i.e only the nuclear genome or it takes into account all the organelles like mitochondrion, cholorplast, etc.

Actually we would like to publish a new genome, but I don't know if I have to include the organelle genes into my gene count. What will be the best way to present the thing in your opinion ?

If I say something like "We found XXX genes in the genome of species A ", would people think by default that all organelles genes are included too ? or the opposite ? I have the impression it is really fuzzy in general...

Your comments are most welcome...

Cheers

[venu]

Few days back I came across this. Just in case if it helps

Answer 1

[TriS]

short answer: include it.

genome refers to the collection of all genes/genetic info in an organism, no matter if it comes from within or outside the nucleus. a simple example is mitochondrial DNA. it is included in the human reference genome and it is annotated as M/MT. I would include it and make sure that the annotation is properly made to address this "issue".

[Juke34]

That seems clear enough. It's what I thought but I didn't remember any clear statement about it. Thank a lot

[Juke34]

Maybe in some symbiosis organismes with many organelles/plasmid around it would be trickier to decide what to separate/include...

[GenoMax]

Symbiotic organisms would represent two distinct genomic entities so would need to be described as separate genomes (with some additional metadata if one can't independently survive without the other).