From: "Garth I. Patterson" <patterson@waksman.rutgers.edu>
Date: Fri Oct 17, 2003 7:50:39 AM US/Pacific
To: Paul Sternberg <pws@caltech.edu>, <scott.baird@wright.edu>,
<dave.pilgrim@ualberta.ca>, <arose@gene.nce.ubc.ca>, Mark Viney
<Mark.Viney@bristol.ac.uk>, Mark Blaxter <mark.blaxter@ed.ac.uk>
Subject: Re: nomenclature, non-elegans
Dear Paul,
It seems you have proposed a way to be sure that briggsae names will
not
match C. elegans names unless the genes are orthologs. So cb-dpy-1 is
the
ortholog of elegans dpy-1, but dpy-cb2 is not an ortholog of elegans
dpy-2.
But that allows us to end up with the following--cb might have a gene
called
dpy-cb2, or cb-dpy-cb2 as a synonym, and a second gene called
cb-dpy-2. The
names are unique, but perhaps confusing. Maybe genes defined only by a
mutant phenotype in briggsae should get a unique number, so that
briggsae
and elegans genes only have the same number if they are orthologs.
Whoever
hands out "dpy" numbers would do so for all species. I am putting this
out
there for comment--it removes one problem and replaces it with
another. On
balance I like the idea, but can see the other side.
Also, it might make sense to make a rule now about renaming genes. If
there
is a gene that is called dpy-cb40 that turns out to be an ortholog of
dpy-20, should it be renamed cb-dpy-20 as a matter of course?
Whoever hands out three letter gene names should do so for briggsae,
for
consistency.
Garth