Subject: Re: nema genetic nomenclature
From: Bhagwati P Gupta
Date: Sun, 27 Oct 2002 14:52:11 -0800
To: Jonathan Hodgkin , Paul Sternberg
CC: tinoue@its.caltech.edu, Eric Haag , ralf.sommer@tuebingen.mpg.de, riddled@missouri.edu, dbaillie@gene.mbb.sfu.ca, Marie-Anne Felix , Victor Ambros , CGC advisory , greenwald@cancercenter.ccc.columbia.edu, ikatsura@lab.nig.ac.jp, jorgensen@biology.utah.edu, kjk1@cornell.edu, leon@eatworms.swmed.edu, sstrome@bio.indiana.edu, Thomas.Burglin@biosci.ki.se, Bhagwati P Gupta

Hello All,
    Jonathan's suggestions on Paul's proposals look very good. Regarding proposal#2 I think that mixing gene classes between C. elegans and other species (for example, dpy-34 for a C. briggsae Dpy and dpy-35 for a future C. elegans Dpy) would be confusing.  Considering that Dpy mutations may also be generated in other species, it would cause even more mixing of numbers. Hence it might be a good idea to reserve number blocks for at least C. elegans genes. Other species may have overlapping gene numbers, e.g., dpy[cb]-101 in C. briggsae and dpy[cr]-101 in C. remanei, for different Dpy genes and be distinguished by their two digit species names. C. elegans would always serve as reference for comparative studies.

Bhagwati
 
 

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

----------------------------------------------------
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
Email jah@bioch.ox.ac.uk
Nomenclature Guidelines:
http://biosci.umn.edu/CGC/Nomenclature/nomenguid.htm 


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Bhagwati P Gupta
Biology 156-29, Caltech
Pasadena, CA 91125
Phone: 626-395-8391 (lab)