Gene Nomenclature Guide

• Format of gene names
• Choosing a gene name
• Changing a standard gene name
• Format of C. albicans gene names
• Format of C. glabrata gene names
• Format of Standard tRNA Names
• Detailed format of gene, protein, and allele names

The 3-letter gene symbol should stand for a description of a phenotype, gene product, or gene function. In addition, it is strongly preferable that a given gene symbol have only one associated description (i.e., all genes which use a given 3-letter symbol should have a related phenotype, gene product, or gene function, and that 3-letter symbols have the same meaning for S. cerevisiae and Candida genes). Where Candida and S. cerevisiae genes appear to be orthologous, it is preferable that they share the same gene name. Where Candida and S. cerevisiae genes are similar, but the function of these genes is not the same in both species, it is preferable that the genes do NOT share a name; rather, the gene name assigned should have some significance with respect to the function of the gene.

There are some gene names with non-standard gene format that are currently in use in CGD. Many of these gene names are historical, and are well-recognized within the research community (e.g., C. albicans WH11; OP4; MTLA1; ADE5,7 or C. glabrata UPC2A; MT-II; MT-IIB). Some other genes acquired a non-standard name when the name was used in a publication describing a large-scale experiment (e.g., C. albicansFESUR1, CAM1-1).

Going forward, it is preferable that newly named genes use standard format whenever possible. New, nonstandard gene names will be added to CGD as aliases, but not as Standard Names. (Exceptions may be made in cases where the S. cerevisiae ortholog has a nonstandard-format Standard Name in SGD for historical reasons.)

Species prefixes (e.g., "Ca" or "Cg") used in front of a gene name is not part of the true gene name. The use of prefixes adds clarity to papers discussing genes from different species that share a name (e.g., CaURA3 vs. ScURA3), but the gene names themselves do not include the prefix.

At CGD, we curate gene names that have appeared in the published literature; we do not assign names for protein-coding genes, ourselves. CGD collects all published names for each gene; any names in addition to the standard gene name are present in the database as searchable gene aliases. Gene names or locus tags that appear only in GenBank may be used as aliases in CGD; they are not used as standard gene names unless they appear in the published literature.

For C. albicans, CGD also includes the gene identifiers assigned during Assembly 4 and Assembly 6, as well as the IPF and CA identifiers from CandidaDB (d'Enfert et al., 2005). Unpublished gene names that were assigned by CandidaDB based on homology, are included as aliases in CGD. The Suggested Names assigned by the Annotation Working Group are only adopted by CGD upon publication of these names in the scientific literature.

CGD has implemented a gene name reservation system. Reservation of a gene name prior to publication allows other groups to begin using the name as soon as possible, and reduces the likelihood that a gene will acquire multiple distinct names that are used in the published literature. Please use the CGD Gene Registry to reserve new gene names.

Systematic names introduced with Assembly 22 follow a new positionally based systematic nomenclature for chromosomal features. The new systematic name is based on the known chromosomal location and haplotype, and it consists of the chromosome (C1-C7 or CR), a unique number indicating the order of features along chromosomes, the strand (W for Watson or C for Crick) and the haplotype (A or B). For example, C4_03570W_A denotes a feature located on chromosome 4, Watson strand and haplotype A. Feature numbers start at the left end of the chromosome and increase by 10 to allow for adding new features in the intervening spaces as they are discovered.

Systematic names used in previous assemblies were the "orf19.#" names (where "#" is an integer) assigned to open reading frames identified in Assembly 19 of the genome sequence. The Annotation Working Group has assigned orf19 identifiers to some open reading frames that were not part of the original assembly (described in Braun et al., 2005). New orfs have been assigned names of the format "orf19.#.n", where "orf19.#" corresponds to the identifier of the upstream orf19, and "n" is an integer. For example, orf19.5006.1 is located on Contig19-10216 between orf19.5006 and orf19.5007.

Please note that names of the format "orf19.#" are expressed in a slightly different format in the locus_tag field of the GenBank records that are associated with release of Assembly 19. The locus_tag "CaO19.#" is equivalent to the systematic name "orf19.#" (i.e., orf19.5197 and CaO19.5197 refer to the same ORF). In order to facilitate searching for alternative aliases, regardless of their format, the "CaO19.#" identifiers are included in CGD, in addition to the "orf19.#" names.

C. albicans Assembly 20 and Assembly 21 continued to use the orf19 names and they persist in the literature. To facilitate seamless transition between the two nomenclature systems, the former orf19 systematic identifiers are fully searchable and prominently displayed on the Locus Summary pages. The mapping between all orf19 and Assembly 22 identifiers is also available for download here.

Format of systematic tRNA names

The format of C. albicans systematic tRNA names is identical to that of standard tRNA names, described below.

IPF identifiers

C. albicans gene identifiers of the form "IPF#.n" have been assigned at CandidaDB, where IPF stands for "Individual Protein File," "#" is an integer, and "n" is a version number or an informational tag (described in d'Enfert et al., 2005). CGD currently includes the IPF names that were archived in the Annotation Working Group's annotation file as of February 22nd, 2005, some IPF names that CGD curators gathered from the published literature, as well as IPF names retrieved directly from CandidaDB. Where IPF identifiers have been assigned both to an orf and also to its allele, CGD includes both IPF identifiers as searchable aliases on the Locus page.

A cautionary note about suffixes appended to gene names

Aliases from Assemblies 4 and 6

The format of the C. glabrata systematic gene names comes directly from the nomenclature used by the sequencing project, as described by Dujon et al. (2004):

"All annotated genetic elements were designated using a new nomenclature system (http://cbi.labri.fr/Genolevures). Briefly, elements are numbered serially along each sequence contig or scaffold from the left to right of each chromosome using 11 incremental steps (to limit errors and offer the possibility for subsequent insertion of newly recognized elements). The element nomenclature indicates the species (four letters), the project or strain number (one numeral), the chromosome (one letter) followed by the serial number (for example, CAGL0G08492g). The suffix identifies the type of element ('g' stands for any element whose RNA product may be translated by the genetic code; 'r' for elements whose RNA product is not translated; 's' for a cis-acting element; and 'v' for intergenes (intervening))."

Format of systematic tRNA names

C. glabrata systematic tRNA names follow the sequencing project systematic naming conventions, described above.

tRNAs annotated in the sequencing projects were confirmed by CGD using the program tRNAscan-SE. The eukaryotic model option was used for nuclear tRNAs, and the organeller model was used for mitochondrial tRNAs. Instances of disagreement between the original annotations and tRNAscan-SE were resolved by alignment with experimentally verified tRNAs from S. cerevisiae.

CGD uses the following format for standard tRNA names: 't' + encoded amino acid [one-letter code] + (anticodon) + count. For example, tQ(CUG)2 for the second instance of tRNA-glutamine with anticodon 'CUG'. Mitochondrial tRNAs use the same format, but are appended by 'mt': for example, tH(GUG)4mt. The count for mitochondrial tRNAs is continued from those of nuclear-encoded tRNAs of the same coding type. To facilitate searching, an alias is provided with each 'U' replaced by 'T' in the anticodon.

Please note that the count suffix is arbitrary, and independent among the different species in CGD. It is used simply to create a unique identifier for each tRNA gene of a given species, and no special relationship between two tRNAs with the same standard name from different species is implied. For example, the tH(GUG)1 tRNA gene in C. albicans and the tH(GUG)1 tRNA gene in C. glabrata are not necessarily expected to be more closely related to each other than to any other tH(GUG) in either genome.

For species-specific, systematic tRNA names, please see the gene-naming section for the particular species, above.