From: Ronald E Ellis <ron.ellis@umdnj.edu>
Date: Mon Oct 20, 2003 07:01:26 AM US/Pacific
To: Paul Sternberg <pws@caltech.edu>
Subject: Re: nomenclature non-elegans genetic

Dear Paul,

Thanks for sending this draft, and also the series of comments people have submitted.  I think we are all reasonably close to a consensus.  However, I do have a few suggestions:

(1) I agree completely with your proposal for naming orthologs.  We have used this convention in our own publications.  For example, we call the C. remanei ortholog of fog-3:  Cr-fog-3.

I don't think that two-letter designations will be a problem for the developmental community, but understand the concerns raised by our colleagues, and would be happy to go to a three-letter designation for each species, if that is the consensus of the community.

(2) I agree with using standard C. elegans nomenclature and lab designations to name alleles, insertions, and so forth.

(3) I disagree with creating gene names like dpy-cb1.  Three things about this system bother me:

  (a) The gene names become long and cumbersome.

  (b) There is potential for confusion between genes like Cb-unc-4 and unc-cb4.  Researchers outside of our community already complain about nematode nomenclature.  I think this system would make our work even less accessible.

  (c) Some C. elegans gene names strike many of us a problematic in their own right.  For example, the "unc" designation covers over vast differences in phenotype, and almost every non-C. elegans researcher I have spoken with tells me that they have trouble keeping track of the different uncs.

Thus, for naming genes that do not have a known ortholog, I propose using a novel gene name, not employed in any other species.  Rather than being scripted, this could be done along the lines of Drosophila genetics.

For example, I just isolated a C. remanei mutant that could be called Unc, according to classic C. elegans nomenclature.  I have no idea what the ortholog of this gene is in C. elegans, so I could call it unc-cr1, according to your suggestions.  But I would prefer a name like lpy-1 for "loopy", since that description gives a clearer picture of what is wrong with the animal's movement.

Thanks,

Ron

Dear friends, I think we have reasonable convergence on a nomenclature plan.  (The immediate motivation is to get briggsae genetic information into wormbase; there are now many mutations and loci).   (Some of you have already bought on in Spring-Summer 2002 when this first came up).   One briggsae-specific question is what we want to use for species identifiers (dpy-cb1 rather than dpy-b1, etc.)  Comments? After dealing with your comments, this will get posted on WormBase, Society of Nematology, etc.   Thanks Paul Revised genetic nomenclature for non-C. elegans nematode species   DRAFT 2003-10-16  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 that does not overlap with other species. e.g., the C. briggsae equivalent of dpy is cby, and 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, but with a species-specific identifier.   The proposal: 1.  Orthologs will be given the same name but with a species prefix.  For example, cb-tra-1 is 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.  For paralogs, a "dot and number" can be appended to distinguish paralogs,  e.g., hsp-16.1, hsp-16.2. 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 symbol as a postfix to the number.  The symbol will include one or more letters followed by a number. For example, C. briggsae genes could be dpy-cb1 OR dpy-B1 OR dpy-CAENORHABDITISBRIGGSAE000000001 etc.  The organism's community should decide on the exact implementation; this choice will be tracked by the CGC or WormBase.  A species prefix could be added but will be redundant, e.g., cb-dpy-cb1 OR cb-dpy-B1.  OR ce-dpy-1.   C. briggsae gene tra-cb1 does not necessarily correspond to C. elegans tra-1, tra-2 and tra-3. 2a.  We propose that dpy-cb1 be the form for C. briggsae since lower case is easier to type.  (Paul Sternberg, Bhagwati Gupta have so far expressed this preference.) 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, transgenes, and other variants, unique numbers (unique across all species) 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, "syIs802" is an integrated transgene in C. briggsae from the Sternberg laboratory; it could be referred to as cb-syIs802.   syIs802will never be used for something else, especially a C. elegans transgene. Existing gene classes used in other species could be retained since there are not too many of them (e.g., ped), but should be retired if possible.   4a.  We propose that the C. briggsae classes be retired  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.) Notes. Bird and Riddle (1994 J. Nematol.) proposed nomenclature for parasitic nematodes.  They suggested following the C. elegans guidelines but with designations in parallel.  It would be desirable for one source (CGC/Wormbase) to enforce uniqueness of lab and allele designations.   Philosophy and constraints:   a. From an informatician's perspective, each genetic entity should have a unique name, and there should be an authority to maintain uniqueness.   b. From a researcher's perspective, the names should be easy-to-use and intuitive, and not generate confusing nicknames (think about what you would write on the side of your Petri plate). Sub-communities (e.g., those working on Pristionchus or C. briggsae) would tend to drop lengthy identifiers.   c. If possible, the names should not stifle creativity. d. From a classical geneticist's point of view, there should be names that can be used for decades before the molecular identity of a locus is known. e. From a molecular geneticist's point of view, orthology should be obvious from the name.  There can multiple homologs for a gene, and orthology might not be clear, especially if full genome sequence is not available.   f. However, the name should not confuse relationships among genes.  g. Other species names should not crowd out those in C. elegans. Uniqueness (a) is the overriding concern.  Ease of use is the second priority.  Depending on the researcher, (b,d)  or maximizing (e) and minimizing (f) is more important.  N. B.   There are millions of nematode species.   Paul W. Sternberg HHMI and Division of Biology 156-29, Caltech 1200 E. Calif Blvd., Pasadena CA 91125 tel 626-395-2181    fax 626-568-8012    email pws@caltech.edu Admin. Assistant Mary Alvarez 626-395-3990  alvarezm@caltech.edu Lab webpage:  http://wormlab.caltech.edu WormBase:      http://www.wormbase.org Worm Literature Search Engine:  http://www.textpresso.org



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Ronald Ellis
Associate Professor of Molecular Biology
The UMDNJ School of Osteopathic Medicine
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