Subject: Re: nema genetic nomenclature
From: Susan Strome
Date: Mon, 28 Oct 2002 21:22:18 -0500
To: jonathan.hodgkin@bioch.ox.ac.uk, pws@caltech.edu
CC: tinoue@its.caltech.edu, Bhagwati Gupta , Eric Haag , , , , Marie-Anne Felix , Victor Ambros , CGC advisory , , , , , ,

Dear All:  Most of the nomenclature issues sound pretty well agreed upon, except naming new genes in non-elegans species before homology information is known.  I am going to weigh in with Jonathan's initial suggestion to use allele names, such as  Cb-dpy(e2831).  If the "subcommunities" think that that system will be too cumbersome, then dpy-cb1 or dpy-b1 seems like the second best option - but it suffers from a future renumbering, if orthology is discovered with an existing C. elegans dpy gene (dpy-cb1 may become Cb-dpy-5).  I definitely vote against numbering new Cb dpy genes from where the Ce dpy genes left off, such as Cb-dpy-34.

Susan


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



On Sat, 26 Oct 2002, Paul Sternberg wrote:

 I have revised the nomenclature guideline draft after everyone's
 comments last June.
 We would like to try to get something in to the WBG.  What do you think?
 Thanks.
 Paul

 Revised nomenclature for non-C. elegans nematode species  DRAFT
 2002-10-26

 Under the current nomenclature system for non-C. elegans nematode
 species, each gene class in a given species has a unique three-letter
 gene class name which does not overlap with other species. e.g. the C.
 briggsae equivalent of dpy is cby, the equivalent of unc is mip.
 However, with over 1100 gene classes in C. elegans and an increasing
 number of species under study, this will soon become unmanageable.  We
 > therefore propose an alternative nomenclature system that will allow
 genes with similar mutant phenotypes in other species to keep the same
 gene class name.

 1.  Orthologs will be given the same name but with a species prefix.
 For example, Cb-tra-1 for the C. briggsae ortholog of C. elegans tra-1.
 In some cases, there will be paralogs and some confusion; we expect this
 to be minor compared to the convenience of having orthologs having the
 same names.

 2. When a gene is identified in another species that belongs to a gene
 class with a clear equivalent in C. elegans, it should be given the same
 gene class name, but with a unique number.   For example, the next C.
 briggsae dpy mutation will be assigned ždpy-31'".   A species prefix can
 be added but will be redundant, e.g., Cb-unc-132.

 3.  Gene classes with no equivalent in C. elegans or other species will
 be given unique three-letter-number names.

 4.  For alleles, strains, polymorphisms, rearrangements, unique numbers
 will be assigned by the relevant laboratory using the standard C.
 elegans nomenclature.  In all cases, a species prefix can be used, but
 is redundant.  For example, žsyIs701Ó is an integrated transgene in C.
 briggsae from the Sternberg laboratory; it could be refered to as
 Cb-syIs701.

 Responsibility for the numbering of a gene class will reside with the
 assigning laboratory, unless transferred by them to WormBase and the
 Caenorhabditis Genetics Center.  (As in the present practice, in some
 cases, if desirable, a small block of numbers can be assigned to another
 laboratory. )

 signatories: (Hopefully)
 Jonathan Hodgkin, Ralf Sommer, David Baillie, Donald Riddle, Takao
 Inoue, Bhagwati Gupta, Marie-Anne Felix, Paul Sternberg,  etc. (Eric
 Haag, Ronald Ellis, David Fitch, Victor Ambros÷.) Others?



-- 
Susan Strome
Dept. of Biology
Jordan Hall 142
1001 E. Third Street
Indiana University
Bloomington, IN  47405-3700
phone: 812-855-5450
FAX: 812-855-6705
email: sstrome@bio.indiana.edu