Subject: Re: nema genetic nomenclature
From: Iva Greenwald
Date: Mon, 28 Oct 2002 09:38:27 -0500
To: Jonathan Hodgkin
CC: Paul Sternberg ,, Bhagwati Gupta , Eric Haag ,,,, Marie-Anne Felix , Victor Ambros , CGC advisory ,,,,,,,

Dear colleagues,

I appreciate the issue Jonathan has raised with respect to point 2.  
However, I also see the drawbacks to using the form "Cb-dpy(allele)" for
genetically defined genes.   I have never participated in discussions of
these issues before, but was any thought ever given to modifying the
gene names, e.g. C. briggsae dpy genes could be dpy-Cb1, dpy-Cb2, etc.
or dpy-A1, dpy-A2 (with each species being given an arbitrary one or two
letter code)?  That would avoid confusion but be more compact, and
facilitate the handling of multiple alleles...

Best regards,

Jonathan Hodgkin wrote:
Dear colleagues

Some comments on Paul's proposals:

Proposals 1 and 4 are straightforward and reasonable.

Proposal 3 is also fine, with the stipulation that new 3-letter
names should be checked for availability and acceptibility by
WormBase or CGC.  Otherwise, the same 3-letter names are likely
to be used for different purposes in different species.

Proposal 2 has problems.  An apparently new Cb-dpy may turn out to be
the ortholog of (for example) Ce-dpy-3, after a bit of work has
been done on it, so prematurely calling it dpy-34 (which is currently
the next available dpy- number) would not be a good idea.
I would be hesitant about promiscuously assigning lots of new dpy-
genes, in the absence of any certain information on lack of
orthology with existing Ce-dpy- genes.  However, generating such
information may not be easy and will certainly take time.

As suggested previously, one way to deal with this problem is
to give provisional names based on the defining mutant allele.
So a new Cb dumpy mutation that we have, e2831, would define
dpy(e2831).  And one isolated in the Sternberg lab, say sy5432,
would define dpy(sy5432).  These provisional names would
therefore be unique and unambiguous, and could be published as such.
If it later became clear that these did not correspond
to known Ce-dpy genes, then it would certainly be appropriate to
give them new dpy- numbers, dpy-34 and dpy-35 (or just dpy-34,
if they turned out to be allelic).
This tactic is already used in the Ce literature, when authors are
not certain whether a mutation defines a new gene or not.

I have cc'ed this reply to the CGC advisory group, who may have
useful input.

Best wishes


Jonathan Hodgkin
CGC Genetic Map and Nomenclature Curator
(Caenorhabditis Genetics Center Subcontract)
Genetics Unit, Department of Biochemistry
University of Oxford
South Parks Road, Oxford OX1 3QU, UK
Tel (+44) 1865 275317
Fax (+44) 1865 275318
Nomenclature Guidelines:

On Sat, 26 Oct 2002, Paul Sternberg wrote:

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

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

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?

-- Iva Greenwald HHMI/Dept. of Biochemistry and Molecular Biophysics Columbia University, College of Physicians and Surgeons 701 West 168th Street, Room 720A New York, NY 10032 tel: (212) 305-6928/6931 FAX: (212) 305-1721 e-mail: