Hello, I am wondering about best practices for N2 worms.
Our lab recently ordered a new stock of N2 from the CGC. This stock contains the alh-2(ot588) mutation as indicated in the CGC description. Our old laboratory stock of N2 (around 10 years old) does not seem to have this mutation. Does anyone know what is the best practice for N2 worms, use of our old stock without the ot588 mutation or use of the new stock with the mutation?
Thank you!
Best practice is to use the strain that’s isogenic/most similar to the other strains that you’re working with. In most cases, that will be the laboratory N2.
Even canonical N2 strains are known to vary considerably in basic properties like lifespan and fecundity (e.g., see this 2001 article in Worm Breeder’s Gazette http://wbg.wormbook.org/wli/wbg16.5p24/), and genetic drift occurs in the lab as the strain is propagated over the years. It’s only the availability of whole-genome sequencing that now allows us to identify that variation at the molecular level.
It could be worse; be grateful you’re not working with flies…
The lab-to-lab variation in N2 has long been a concern, and there is not a reference stock that perfectly matches the complete genome. In 2019, strain PD1074 was introduced as a wild-type reference strain with a complete corresponding genome (https://cgc.umn.edu/strain/PD1074). The strain is a derivative of N2 and was carefully sequenced to provide complete coverage (https://pubmed.ncbi.nlm.nih.gov/31123080/). Before receiving the strain at the CGC, we consulted with collaborators to devise a strategy for maintaining stocks of the strain in a manner that will minimize drift while preserving original frozen aliquots well into the future. Essentially, the strain provides a chance for labs to reset the clock and start with a true reference strain. Reactions to PD1074 have been mixed. Some labs have been excited about the “new N2” or “N2 2.0” whereas others were reluctant to switch because all of their strains and prior work was generated in their N2 background. The new strain seems to be most popular with more recently established labs and those labs focused on genomics. Some users have commented on differences they’ve noticed between PD1074 and classic N2, such as brood size, gonad morphology, etc. We are not offering a PD1074 male stock at this time (as we do for N2 Male) because we don’t want to pass additional generations while crossing to maintain them and end up in the same situation with divergent strains.
If one is concerned about drift in your lab’s reference wildtype strain - whichever you choose - a practice I’ve heard is the following: When you first acquire the strain, grow a very large culture, and freeze down a lot of aliquots. Then, at some time interval, like a year or two, everyone in the lab discards their wildtype, and starts over with worms from a freshly thawed aliquot.