Subject: Re: nema genetic nomenclature
From: Erik Jorgensen
Date: Mon, 28 Oct 2002 06:46:08 -0700
To: "Ralf. J Sommer"
CC: Bhagwati P Gupta , Jonathan Hodgkin , Paul Sternberg ,, Eric Haag ,,, Marie-Anne Felix , Victor Ambros , CGC advisory ,,,,,,

Hi Ralf (and others),

I understand your issue here -- it is unlikely you will ever clone these dpy's but you need to use them to map and to communicate with other labs.   You probably have a half dozen alleles of some of these dpy genes.  On the other hand you eventually will clone some of them and then Pp dpy-1 will end up being an ortholog of Ce dpy-5.  That would be unfortunate we need to have a common language.  I think Jonathan's proposal takes care of this issue, but I agree it leads to some clumsiness.  I still think you can refer to genes with multiple alleles by the reference allele name.  Thus, Cb-dpy(e2831) becomes the reference allele; to establish that new Dpys are allelic one needs to perform a complementation test anyway, and thereafter one could state that sy5432 is an allele of  dpy(e2831).  One should use the reference alleles for standard genetics whenever possible.  However, it becomes difficult for genes in which studying multiple alleles is important.  What do you do when you publish a genetic characterization of a complex locus in Pristionchus affecting vulval development and you have no idea what the ortholog is?  In these cases I would favor assigning a new three letter code specific to Pristionchus.  If the molecular biology is performed before publication of the new three letter gene name then the name reverts to the elegans gene name.  This plan would still cause a slow proliferation of gene names but it would minimize confusion.
Erik Jorgensen

On Monday, October 28, 2002, at 04:36 AM, Ralf. J Sommer wrote:

Hello All,

I like the proposal but agree with Bhagwati´s and Paul´s argument:
Lets take Pristionchus as an example. We have carried out a large
scale screen for dpy mutants and have at least 12 complementation
groups. Although I am not sure what we will do and how far we will
get in identifying these genes molecularly, we don´t even know if the
same genes are mutated to result in dpy phenotypes. Therefore, the
concept of renaming does not really help so much for a categorie such
as dpy or unc.

One simple solution would be to use the species prefix and start to
count by one in each species: Cb-dpy-1 etc. That would also allow
"sub-communities" to easily communicate with regard to the numbering
in those species.


Ralf J .Sommer
Dept. for Evolutionary Biology
Max Planck Institute for Developmental Biology
Spemannstrasse 37
Tuebingen D-72076, GERMANY
Tel: +49-7071-601371