NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

Riddle DL, Blumenthal T, Meyer BJ, et al., editors. C. elegans II. 2nd edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 1997.

Cover of C. elegans II

C. elegans II. 2nd edition.

Show details

Part AGenetic Nomenclature

The genetic nomenclature summarized here is based on the original proposals for Caenorhabditis elegans nomenclature (Horvitz et al. 1979), plus additional recommendations that have been distributed in The Worm Breeder's Gazette.

Genetic Loci

Genes are given names consisting of three italicized letters, a hyphen, and an arabic number, e.g., dpy-5 or let-37 or mlc-3 . The gene name may be followed by an italicized Roman numeral, to indicate the linkage group on which the gene maps, e.g. dpy-5 I or let-37 X or mlc-3 III.

For genes defined by mutation, the gene names refer to the mutant phenotype originally detected and/or most easily scored: dumpy (DumPY) in the case of dpy-5 , and lethal (LEThal) in the case of let-37 .

For genes defined by cloning, on the basis of sequence similarity, the gene name refers to the predicted protein product or RNA product: Myosin Light Chain in the case of mlc-3 , SuperOxide Dismutase in the case of sod-1 , Ribosomal RNA in the case of rrn-1 .

Genes with related properties are usually given the same three-letter name and different numbers. For example, the 3 known myosin light chain genes are indicated mlc-1, mlc-2, mlc-3, and the more than 20 different dumpy genes are indicated dpy-1, dpy-2, dpy-3, and so on.

There are no specific recommendations for designating cloned sequences that are not homologous to known genes. Most genomic clones have been provided by the C. elegans mapping/sequencing consortium (based at the Sanger Centre, Cambridge, UK, and the Genome Sequencing Center, St. Louis, USA; see Waterston et al., this volume). Cosmid clones generated by the consortium are named on the basis of the vector, either pJB8 (initial letters B, C, D, E, R, M, ZC) or a Lorist vector (initial letters K, T, W, F, ZK). Phage clones (in Lambda 2001) are identified by the initial letters A, ZL, YSL. YACs (yeast artificial chromosome clones) are identified by the initial letter Y, e.g., Y3D5.

Sequences that are predicted to be genes are named on the basis of the sequenced cosmid, plus a number. For example, the genes predicted for the cosmid T05G3 are called T05G3.1, T05G3.2, etc. DNA clones that have not been generated by the consortium are usually designated by the laboratory strain designation (see below), a # symbol and an isolation number, e.g., MT#JAL6.

Homologous Genes

If a homolog of a known C. elegans gene is identified in a related species such as Caenorhabditis briggsae, it can be given the same gene name, preceded by two italic letters referring to the species, and a hyphen. For example, Cb-tra-1 is the name for the C. briggsae homolog of the C. elegans gene tra-1 .

The C. elegans homolog of a gene identified and named in another organism can be distinguished by the same convention, using "Ce-" as an optional prefix. For example, Ce-snt-1 defines the C. elegans synaptotagmin gene.

Alleles and Mutations

Every mutation has a unique designation. Mutations are given names consisting of one or two italicized letters followed by an italicized Arabic number, e.g., e61 or mn138 or st5. The letter prefix refers to the laboratory of isolation, as registered with the Caenorhabditis Genetics Center (CGC). There are currently more than 150 registered laboratories (see Part B). For example, e refers to the MRC Laboratory of Molecular Biology (Cambridge, U.K.), and st refers to the laboratory of R.H. Waterston (Washington University, St. Louis, Missouri).

When gene and mutation names are used together, the mutation name is included in parentheses after the gene name, e.g., dpy-5(e61), let-37(mn138). When unambiguous, e.g., if only one mutation is known for a given gene, gene names are used in preference to mutation names ( let-37 rather than mn138).

Suffixes indicating characteristics of a mutation can follow a mutation name. These are usually two-letter nonitalicized letters, e.g., hc17ts, where ts stands for temperature sensitive.

The wild-type allele of a gene is defined as that present in the Bristol N2 strain, stored frozen at the CGC and other locations. Wild-type alleles can be designated by a plus sign immediately after the gene name, dpy-5+, or by including the plus sign in parentheses, dpy-5(+). The widely understood convention of a superscript plus sign, dpy-5 +, has also been used.

There is no special nomenclature for suppressor mutations. Most extragenic suppressor loci are called sup (40 loci defined so far, with a wide variety of properties and mechanisms). Some more specific classes have been established, such as smu (Suppressor of Mec and Unc), and smg (Suppressor with Morphogenetic effect on Genitalia). Intragenic suppressors or modifiers are indicated by adding a second mutation name within parentheses; for example, unc-17(e245e2608) is an intragenic partial revertant of unc-17(e245).

Mutations known to be chromosomal rearrangements, rather than intragenic lesions, are named somewhat differently, as described below.

RFLPs

Polymorphic sites, which are usually RFLPs (restriction fragment length polymorphisms), are designated by an italic letter P and an italic number, preceded by the allele prefix for the laboratory responsible for identifying the site. For example, eP2 and eP98 are RFLPs identified at the MRC Laboratory of Molecular Biology, and stP17 and stP196 are RFLPs identified in the laboratory of R. H. Waterston.

Transgenes

Transformation of C. elegans with exogenous DNA usually leads to the formation of a transmissible extrachromosomal array containing many copies of the injected DNA, but sometimes chromosomal integration of the injected DNA can occur. Extrachromosomal arrays are given italicized names consisting of the laboratory allele prefix, the two letters Ex, and a number. Integrated transgenes are designated by italicized names consisting of the laboratory allele prefix, the two letters Is, and a number. Both Ex and Is can optionally be followed by genotypic or molecular information describing the transgene, in brackets, e.g., eEx3 or eIs2 or stEx5 [sup-7(st5) unc-22(+)].

Genotypes

Mutants carrying more than one mutation are designated by sequentially listing mutant genes or mutations according to the left-right (= up-down) order on the genetic map. A skeleton genetic map is provided in Part C. Different linkage groups are separated by a semicolon and given in the order I, II, III, IV, V, X, f. IV are the five autosomes, X is the X chromosome, and f refers to free duplications or chromosomal fragments. For example: dpy-5(e61) I; bli-2(e768) II; unc-32(e189) III .

Heterozygotes, with allelic differences between chromosomes, are designated by separating mutations on the two homologous chromosomes with a slash. Where unambiguous, wild-type alleles can be designated by a plus sign alone, or even omitted, e.g., dpy-5(e61) unc-13(+)/dpy-5(+) unc-13(e51) I can also be written dpy-5 +/+ unc-13 or dpy-5/unc-13.

Transposons

C. elegans transposons are called Tc1, Tc2, etc., where each number represents a different family. Transposon names are not italicized except when included in a genotype. Transposon insertions in genes are indicated by adding ::Tc to the relevant mutation name, as an optional descriptor. Thus, a mutation of the gene unc-54 , called r293, is a Tc1 insertion and can therefore be written unc-54(r293::Tc1).

Chromosomal Aberrations

Duplications (Dp) deficiencies (Df), inversions (In), and translocations (T) are known in C. elegans cytogenetics; these are given italicized names consisting of the laboratory mutation prefix, the relevant abbreviation, and a number, optionally followed by the affected linkage groups in parentheses, for example, eT1(III;V), mnDp5(X;f), where f indicates a free duplication. Chromosomal balancers of unknown structure can be designated using the abbreviation C, for example, mnC1 (II).

Phenotypes

Phenotypic characteristics can be described in words, e.g., dumpy animals or uncoordinated animals. If more convenient, a nonitalicized three-letter abbreviation, which usually corresponds to a gene name, may be used. The first letter of a phenotypic abbreviation is capitalized, e.g., Unc for uncoordinated, Dpy for dumpy. If necessary to distinguish among related but distinguishable phenotypes, the relevant gene number can be added, e.g., Unc-4 and Unc-13, to differentiate the distinct phenotypes produced by mutations in the two genes unc-4 and unc-13 . Abbreviations that do not correspond to gene names can also be used, e.g., Muv for multiple vulval development.

A common convention, when comparing a mutant with the wild type, is to use the prefix non- to refer to the wild-type phenotypes, for example, non-Lin (= wild-type cell lineage) or Dpy non-Unc (= wild type with respect to movement, but dumpy with respect to body shape).

Proteins

The protein product of a gene can be referred to by the relevant gene name, written in nonitalic capitals, for example, the protein encoded by unc-13 can be called UNC-13. Where more than one protein product is predicted for a gene (usually as a result of alternative message processing), the different proteins are distinguished by additional capital letters, for example, TRA-1A, TRA-1B.

Strains

A strain is a set of individuals of a particular genotype with the capacity to produce more individuals of the same genotype. Strains are given nonitalicized names consisting of two uppercase letters followed by a number. The letter prefixes refer to the laboratory of origin and are different from mutation letter prefixes (see Part B). For example, CB1833 is a strain of genotype dpy-5(e61) unc-13(e51), constructed at the MRC Laboratory of Molecular Biology (strain prefix CB, allele prefix e), and MT688 is a strain of genotype unc-32(e189) +/+ lin-12(n137) III; him-5(e1467) V, constructed in the laboratory of H.R. Horvitz at M.I.T. (strain prefix MT, allele prefix n).

Some 3-letter laboratory designations are also in use (see Part B), to refer to strains of nematode species other than C. elegans.

Copyright © 1997, Cold Spring Harbor Laboratory Press.
Bookshelf ID: NBK20203
PubReader format: click here to try

Views

  • PubReader
  • Print View
  • Cite this Page

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...