Subject: nema genetic nomenclature
From: Paul Sternberg
Date: Sat, 26 Oct 2002 09:25:14 -0700
CC:, Bhagwati Gupta , Eric Haag ,,,, Marie-Anne Felix , Victor Ambros

I have revised the nomenclature guideline draft after everyone's comments last June.
We would like to try to get something in to the WBG. What do you think?

Revised nomenclature for non-C. elegans nematode species DRAFT 2002-10-26

Under the current nomenclature system for non-C. elegans nematode species, each gene class in a given species has a unique three-letter gene class name which does not overlap with other species. e.g. the C. briggsae equivalent of dpy is cby, the equivalent of unc is mip. However, with over 1100 gene classes in C. elegans and an increasing number of species under study, this will soon become unmanageable. We therefore propose an alternative nomenclature system that will allow genes with similar mutant phenotypes in other species to keep the same gene class name.

1. Orthologs will be given the same name but with a species prefix. For example, Cb-tra-1 for the C. briggsae ortholog of C. elegans tra-1. In some cases, there will be paralogs and some confusion; we expect this to be minor compared to the convenience of having orthologs having the same names.

2. When a gene is identified in another species that belongs to a gene class with a clear equivalent in C. elegans, it should be given the same gene class name, but with a unique number. For example, the next C. briggsae dpy mutation will be assigned “dpy-31'". A species prefix can be added but will be redundant, e.g., Cb-unc-132.

3. Gene classes with no equivalent in C. elegans or other species will be given unique three-letter-number names.

4. For alleles, strains, polymorphisms, rearrangements, unique numbers will be assigned by the relevant laboratory using the standard C. elegans nomenclature. In all cases, a species prefix can be used, but is redundant. For example, “syIs701” is an integrated transgene in C. briggsae from the Sternberg laboratory; it could be refered to as Cb-syIs701.

Responsibility for the numbering of a gene class will reside with the assigning laboratory, unless transferred by them to WormBase and the Caenorhabditis Genetics Center. (As in the present practice, in some cases, if desirable, a small block of numbers can be assigned to another laboratory. )

signatories: (Hopefully)
Jonathan Hodgkin, Ralf Sommer, David Baillie, Donald Riddle, Takao Inoue, Bhagwati Gupta, Marie-Anne Felix, Paul Sternberg, etc. (Eric Haag, Ronald Ellis, David Fitch, Victor Ambros….) Others?