9.0 years ago by
Another thing to consider: we are increasingly realizing that each individual (or clonal population thereof) that is sequenced is proving to contain differences.
The most accepted and acknowledged ones are of course SNPs, but indels and copy number polymorphisms are also very common. In addition to those, there are a lot of rearrangements (at least for organisms with linear chromosomes) and horizontal gene transfers from other individuals/populations...
All this tells me that at some point not too far away we will be considering the sequence of each individual within a species independently from the others. We will eventually need to be able to distinguish between strains.
Note that a strain (especially bacterial) cultivated in vitro for hundreds/thousands of generations is likely to have a different genome from that of the original strain. So even with the same name, it might not be the same.
Today, I haven't seen anyone take this into account in their sequencing/annotating/naming efforts. But I do know that it is an issue in some fields of research, like parasitology. I have seen, at a conference, several attendees verbally fighting over conflicting results. In the end they agreed that although they were using the same "strain", it had been cultivated for a long time and each of their aliquots had certainly evolved very differently.
I would suggest including something in the name to specify which isolate you are annotating.
For that matter, I think Pierre's suggestion may be a good one (URN or URI).