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
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
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. )
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?