Pan- / coregenome studies - exclude plasmids?

Question

[mschmid]

I am doing a pan- / coregenome study comparing different strains of the same bacterial species.

Would you exclude the plasmids from this comparison? If yes/no: what is your reasoning?

I know, this depends on the question and on the type of plasmids. What I can say is that the plasmids are quite small (lower 50kb in general). Also, it might be that some plasmids for some strains are missing.

Or is there a "best practice"? (maybe review or so?)

[Joe]

I'm currently doing a similar thing, and the plasmids are only present in a subset of the species. I've elected to analyse the plasmids separately, but it very much depends on the question I would say. If you're just interested in all possible genes that could be conserved across clades for example, then it wouldn't hurt to include the plasmid as part of the chromosomal analysis. Simple answer is try a few different schemes and see what the data looks like to you I'd say.