Here is an attempt at convergence
based on all the nice arguments. I am particularly swayed by the
wishes of those practicing intense classical genetics on other species
(Ralf, Marie-Anne, Takao, Bhagwati, Eric), and thus think we need to
use a dpy-LETTERSnumbers scheme for classicallydefined genes.
I propose that we submit a draft guidelines to the WBG, and call for
comments, since I am sure we have not run this by all interested
parties. A final version will then be sent to the next Gazette, and
submitted for publication.
We still need some guidelines for orthologs.
Revised genetic nomenclature for non-C. elegans
nematode species DRAFT 2002-10-29
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, and 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.
****Philosophy and constraints:
a. From an informatician’s perspective, each genetic entity should
have a unique name, and there should be an authority to maintain
b. From a researcher’s perspective, the names should be easy-to-use
and intuitive, and not generate confusing nicknames (think about what
you would write on the side of your Petri plate). Subcommunities
(e.g., those working on Pristionchus or briggsae) would tend to drop
c. If possible, the names should not stifle creativity.
d. From a classical geneticist’s point of view, there should be names
that can be used for decades before the molecular identity of a locus
e. From a molecular geneticist’s point of view, orthology should be
obvious from the name. f. However the name should not confuse
relationships among genes.
g. Other species names should not crowd out those in C.
Uniqueness (a) is the overriding concern. Ease of use is the second
priority. Dependingo n the researcher, (b,d) or maximizing (e) and
minimizing (f) is more important.
N. B. There are millions of species.
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. (question: is Cb-tra-1 or Cbtra-1 preferable?)
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 symbol.
The symbol will include one or more letters followed by a number.
For example, C. briggsae genes could be
dpy-cb1 OR dpy-B1 OR
dpy-CAENORHABDITIISBRIGGSAE000000001 etc. The organism’s community
should decide on the exact implementation; this choice will be tracked
by the CGC or WormBase. A species prefix can be added but will be
redundant, e.g., Cb-dpy-cb1 OR
3. Gene classes with no equivalent in C. elegans or
other species will be given unique three-letter-number names. There
could be a standard name class for “classically-defined genes” such as
cdg- or gen- or ?
4. For alleles, strains, polymorphisms, rearrangements, transgenes,
and other variants, unique numbers (unique across all species) 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 referred to as
Cb-syIs701. In this case, syIs701
will never be used for something else, especially a C.
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, Paul Sternberg, Ralf Sommer, David Baillie,
Marie-Anne Felix, Donald Riddle, Takao Inoue, Bhagwati Gupta, Eric
Haag, Erik Jorgensen, Iva Greenwald, Susan Strome, Victor Ambros, ….
TO BE CONSULTED: Ronald Ellis, David Fitch, Mark Viney, Mark
Blaxter, Jim McCarter,….others?
A. Should we allow more letters?
****Arguments (not for inclusion in the draft):
dpy(e1111)(e1112) is not viable for the e1112 allele of dpy(e1111).
Subcommunities can still talk in shorthand.
For example, would use dpy-1 rather than
dpy-CAENORHABDITIISBRIGGSAE000000001 just as I might write ‘d1’ on a
An alternative to the letter/number scheme is to start with dpy-1000
for other species.
If someone has a particularly nice example of real alleles, that would