I've recently improved the genome for a bacterial species I'm working on which has two natural plasmids. I'm familiar with naming conventions in engineered plasmids, but how would you go about naming plasmids that exist in nature?
I've seen various methods of naming and renaming used but little guidance or consistency so thought I would seek some opinions.
Often they are left as unamedplasmid1 and unamedplasmid2 which is I think very unhelpful.
Would you bother naming them? Would you need to rename them when found in a different strain? A) If they were significantly different B) If there were only very few even 5 -50bp difference.
And any other thoughts
Dear Benedict,
It is really up to you how you name any plasmids you have isolated, but a good thought to have in mind is how you are going to refer to them in any publication. Most of the time you might talk about the small plasmid, or the large one, but it is perhaps better to settle on a naming convention right from the start.
In the early days of plasmid surveys and investigation, different research groups were given code letters for the plasmids they were working on - presumably a group of plasmid biologists got into a group at some conference and came up with this idea - but now it is really up to you.
First, if you think it likely that the plasmid is transferable, there is little point in naming it after the host bacterium. Second, if the plasmids are known to be different, it is probably easier to give each a different name. Third, if you or your group are likely to be isolating plasmids from the same environment in the future, initiate a plasmid naming system that can be extended when needed.
I've worked with a group looking at pseudomonad-associated plasmids isolated from sugar beets which were grown at the Oxford University Farm at Wytham and the plasmid series were called 'pQBR'. I'm not sure I recall why this was chosen, other than the fact that 'SBW' for 'Sugar Beet Wytham' had already been used for the pseudomonad strains that were also collected from the same place! (the 'BR' probably refers to 'Beet Rhizosphere but only Mark Bailey or Andy Lilley are likely to remember).
If you have a nifty acronym for the site samples were taken from, or the microbial community, etc, then I'd use that plus a simple numbering system!
Andrew
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