UserGuide:Nomenclature nematode

Genetic Nomenclature for Nematodes

Curation and Supervision

An accepted system of gene nomenclature was established for the nematode Caenorhabditis elegans in the nineteen seventies (see Horvitz et al., 1979 Mol. Gen. Genet. 175: 129-133). This system has been refined and consistently used by the many laboratories (currently over 500, world-wide) engaged in active C. elegans research. The guidelines and recommendations for C. elegans genetic nomenclature are posted on WormBase and are also available from the CGC.

Increasing amounts of genomic and genetic information have become available for other nematode species. Draft complete genome sequences have been generated for several of these other nematodes, some of which are being curated by WormBase. For these organisms, gene naming will also be supervised by WormBase, in order to maximize consistency with C. elegans.

It is recommended that nomenclature in general should follow the principles used for C. elegans, as far as possible.

How to Register a New Gene Class or Gene Name

Investigators wishing to register new gene names for C. elegans should note the summary guidelines below and apply online via the WormBase online Submission Form or by email application to genenames@wormbase.org

Species Prefixes

In order to unambiguously specify the nematode species-of-origin, a 3-letter standard prefix and hyphen can be added to the gene name. Examples: the C. briggsae and Pristionchus pacificus orthologs of C. elegans tra-1 are called Cbr-tra-1 and Ppa-tra-1, respectively.

Prefixes so far used include:

• Cel- = Caenorhabditis elegans
• Cbr- = Caenorhabditis briggsae
• Cre- = Caenorhabditis remanei
• Cbn- = Caenorhabditis brenneri
• Cjp- = Caenorhabditis japonica
• Hba- = Heterorhabditis bacteriophora
• Oti- = Oscheius tipulae
• Ppa- = Pristionchus pacificus

Gene naming: Homologous Genes

Genes predicted from whole genome sequences in other nematode species will, in most cases, have identifiable close homologs in C. elegans, for which approved names already exist. In these cases, the same name should be used as in C. elegans, with the relevant species identifier.

Possible Scenarios

• One-to-one: Where one gene in C. elegans corresponds to a single gene in another nematode species, ortholog naming can be applied automatically. e.g.
  • thoc-1 in C. elegans has a C. briggsae ortholog, Cbr-thoc-1.

• One-to-many: Where one gene in C. elegans is related to multiple genes (paralogs) in another nematode species, these paralogs can be named using additional decimal numbers. e.g.
  • thoc-3 in C. elegans has two C. briggsae paralogs, Cbr-thoc-3.1 and Cbr-thoc-3.2.

• Many-to-one: Where multiple genes exist in C. elegans, but only a single gene in another nematode species, it is recommended that either the most closely similar, or the lowest numbered C. elegans gene, be used to name the single gene, as appropriate.

• Many-to-many: Where multiple closely related genes can be identified in both species, but the phylogenetic relationships of the two sets are complex, new gene numbers can be assigned to the set of genes in the other nematode species, after consultation with genenames@wormbase.org.

• In cases where a standard gene name has not yet been assigned in C. elegans, the gene can be referred to using the cosmid.number identifier for the C. elegans gene, preceded by a species prefix. e.g.
  • the ortholog of C. elegans W01B11.3 in Heterorhabditis bacteriophora can be referred to as Hba-W01B11.3. However, in such cases it will usually be both feasible and desirable to assign a standard name to the C. elegans gene as well, at the same time.

Gene Naming: Non-homologous Genes

It is expected that many genes in other nematode species will lack obvious close homologs in C. elegans, because of loss or substantial divergence during the evolution of C. elegans. These genes can be given new gene numbers, if they belong to an identifiable named class in C. elegans, or else new gene name classes can be established for them. In either case, assignment of an approved name should be made after consultation with genenames@wormbase.org.

Gene naming: Forward Genetics

A significant amount of mutation-based forward genetic analysis is being pursued in nematodes other than C. elegans, in particular using other species of Caenorhabditis (C. briggsae, C. remanei, C. brenneri and others), as well as species of Oscheius and Pristionchus. It is expected that most, but not all, of the mutationally-defined genes discovered in these species will prove to have orthologs with equivalent or similar function in C. elegans, and hence that standard genetic names will have been approved already. Several situations can arise:

1. In cases where the molecular identity is known and orthology is obvious, it is recommended that the C. elegans name be used, with the appropriate species identifier prefix. e.g.
   • Ppa-mab-5 is the Pristionchus pacificus ortholog of C. elegans mab-5.
2. In cases where the molecular identity is not initially known, but the mutant phenotype corresponds to a known C. elegans mutant phenotype, it is recommended that the mutant gene be temporarily defined using the relevant gene class name and the mutation number, in parentheses. e.g.
   • mutation s1270 isolated in C. briggsae confers an uncoordinated phenotype, so the gene is temporarily called unc(s1270) or Cbr-unc(s1270).

Once the molecular identity becomes known, the gene can be given an approved unc- number, using the number of the C. elegans ortholog (if this exists) or a new number (if there is no suitable C. elegans ortholog).

1. In cases where the molecular identity is unknown and the mutant phenotype does not correspond to a known C. elegans mutant phenotype, a new gene class name can be established, following consultation with genenames@wormbase.org in order to ensure that the new name is available and appropriate. e.g.
   • cov = Competence and/or centering Of Vulva abnormal.