From: "Garth I. Patterson" <>
Date: Fri Oct 17, 2003 7:50:39 AM US/Pacific
To: Paul Sternberg <>, <>, <>, <>, Mark Viney <>, Mark Blaxter <>
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