Worm Breeder's Gazette 13(1): 17 (October 1, 1993)

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

C. elegans Nomenclature Guidelines: New Recommendations

Jonathan Hodgkin

(MRC-LMB, Cambridge, England) et al.

Discussion before, during and after the 1993 International C. elegans Meeting led to the following new recommendations:

1. Naming the protein products of genes

For a worm gene called any-1 ,the protein product can be referred to as ' any-1 protein'; but this tends to become cumbersome. The recommended abbreviation for the protein is the capitalized, non-italic, hyphenated gene name: ANY-1 .

For cases where a given gene is known or likely to produce more than one protein product, as a result of multiple promoters, alternative splicing and so on, then these different products can be distinguished by additional capital letters: ANY-1 A, ANY-1 B, ANY-1 C,and so on.

Mutant protein products can be named by the missense change, for example a mutant any-1 protein with a Gly to Asp change at position 467 would be written: ANY-1 (G467D).As usual, subscripts and superscripts are avoided.

2. Naming in vitro mutations

Mutations created by in vitro mutagenesis should get standard allele names.

For cases where a pre-existing genomic mutation is re-created by in vitro mutagenesis, it is still desirable to give the new mutation a new name, because it is hard to be sure of exact equivalence between the old and new alleles.

3. Naming C. elegans genes that have been discovered by sequence similarity to known genes in other organisms

These should be given standard 3-1etters-hyphen-number names, preferably after checking with the Caenorhabditis Genetics Center. Names that include 'c' or 'ce' (standing for Caenorhabditis or C. Elegans) are discouraged, because it will usually be redundant to include the name of the organism, and because this would severely limit the number of possible 3-letter names. There are already some exceptions to this principle, like 'ceh' (standing for C. Elegans Homeobox), but these should not be regarded as good precedents.

For many sequence-defined gene classes, it may be simpler to manage the naming from CGC/Cambridge. Consequently, the 'assigning laboratory' will often be CB.

4. Discussing homologous genes in different organisms

Homologous genes from different species will often have the same name, or very similar names. It is desirable to have the option of distinguishing between them, for the purposes of comparative discussion. In such circumstances, the C. elegans gene can be distinguished by adding 'Ce-' (italics) as an optional prefix, For example, Ce- abl-1 as compared to Dm-abl and Hs-abl (the fly and human equivalents).

This procedure can also be used for homologs isolated from other Caenorhabditis species. Thus, the C. briggsae homolog of lin-3 would be Cb- lin-3 ,and the C. vulgaris homolog would be Cv- lin-3 .