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.)
After dealing with your comments, this will get posted on WormBase,
Society of Nematology, etc.
Revised genetic nomenclature for non-C. elegans
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
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
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
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
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.)
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
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
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
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
f. However, the name should not confuse relationships among genes.
g. Other species names should not crowd out those in C.
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.