Subject: Re: nema genetic nomenclature
From: Takao Inoue
Date: Mon, 28 Oct 2002 22:03:17 -0800 (PST)
To: Iva Greenwald
CC: Jonathan Hodgkin , Paul Sternberg , Bhagwati Gupta , Eric Haag , , , , Marie-Anne Felix , Victor Ambros , CGC advisory , , , , , , ,

Hello everyone,

I agree with the point that referring to genes by the reference allele
(e.g. Cb-daf(sy5417)) is problematic when there are additional alleles of
the gene (sy5418 and sy5419). - Without assigning a gene name, there
isn't a way to describe sy5418 and sy5419 as alleles of this gene within
the context of formal genotype description. daf-cb1, etc., would be an ok
solution to this.

A couple of points I would like to make: First, rigorously demonstrating
orthology for mutationally defined genes in non-elegans species is
sometimes not trivial, and it is likely that the analysis will not be
taken that far for many genes. Second, the number of species analyzed in
this way may become rather large. For example, we are starting screens
for cilium-structure mutations in C. remanei and CB5161, to compare with
C. elegans and C. briggse. It is likely that we won't determine the C.
elegans ortholog of most of the genes we would find. I am hoping for a
nomenclature system which would be able to handle such a situation
without too much difficulty.


Takao Inoue
Sternberg lab
California Institute of Technology
Division of Biology  MC 156-29
Pasadena, CA  91125