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Caenorhabditis nomenclature

Tuli, Mary Ann and Daul, Aric and Schedl, Tim (2018) Caenorhabditis nomenclature. In: WormBook. , pp. 1-14. http://resolver.caltech.edu/CaltechAUTHORS:20180508-123432972

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Abstract

Genetic nomenclature allows the genetic features of an organism to be structured and described in a uniform and systematicway. Genetic features, including genes, variations (both natural and induced), and gene products, are assigned descriptorsthat inform on the nature of the feature. These nomenclature designations facilitate communication among researchers (in publications,presentations, and databases) to advance understanding of the biology of the genetic feature and the experimental utilizationof organisms that contain the genetic feature. The nomenclature system that is used for C. elegans was first employed by Sydney Brenner (1974) in his landmark description of the genetics of this model organism, and then substantially extended and modified in Horvitz et al., 1979. The gene, allele, and chromosome rearrangement nomenclature, described below, is an amalgamation of that from bacteria andyeast, with the rearrangement types from Drosophila. The nomenclature avoids standard words, subscripts, superscripts, and Greek letters and includes a hyphen (-) to separatethe gene name from gene number (distinct genes with similar phenotypes or molecular properties). As described by Jonathan Hodgkin, ‘the hyphen is about 1 mm in length in printed text and therefore symbolizes the 1 mm long worm’. These nomenclature propertiesmake C. elegans publications highly suitable for informatic text mining, as there is minimal ambiguity. From the founding of the CaenorhabditisGenetics Center (CGC) in 1979 until 1992, Don Riddle and Mark Edgley acted as the central repository for genetic nomenclature. Jonathan Hodgkin was nomenclature czar from 1992 through 2013; this was a pivotal period with the elucidation of the genome sequence of C. elegans, and later that of related nematodes, and the inception of WormBase. Thus, under the guidance of Hodgkin, the nomenclature system became a central feature of WormBase and the number and types of genetic features significantly expanded. The nomenclature system remains dynamic, with recentadditions including guidelines related to genome engineering, and continued reliance on the community for input. WormBase assigns specific identifying codes to each laboratory engaged in dedicated long-term genetic research on C. elegans. Each laboratory is assigned a laboratory/strain code for naming strains, and an allele code for naming genetic variation(e.g., mutations) and transgenes. These designations are assigned to the laboratory head/PI who is charged with supervisingtheir organization in laboratory databases and their associated biological reagents that are described on WormBase, in publications, and distributed to the scientific community on request. The laboratory/strain code is used: a) to identifythe originator of community-supplied information on WormBase, which, in addition to attribution, facilitates communicationbetween the community/curators and the originator if an issue related to the information should arise at a later date; andb) to provide a tracking code for activities at the CGC. The laboratory/strain designation consists of 2-3 uppercase letters while the allele designation has 1-3 lowercase letters.The final letter of a laboratory code should not be an “O” or an “I” so as not to be mistaken for the numbers “0” or “1” respectively.Additionally, allele designations should also not end with the letter “l” which could also be mistaken for the number “1.” These codes are listed at the CGC and in WormBase. Investigators generating strains, alleles, transgenes, and/or defining genes require these designations and should applyfor them at genenames@wormbase.org. Information for several other nematode species, in addition to C. elegans, is curated at WormBase. All species are referred to by their Linnean binomial names (e.g,. Caenorhabditis elegans or C. elegans). Details of all the genomes available at WormBase and the degree of their curation can be found at www.wormbase.org/species/all


Item Type:Book Section
Related URLs:
URLURL TypeDescription
https://doi.org/10.1895/wormbook.1.183.1DOIArticle
Additional Information:© 2016 Mary Ann Tuli, Aric Daul, Tim Schedl. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Edited by Paul Sternberg. Last revised November 25, 2015. Published in its final form August 8, 2018. This work is funded by U41 HG002223D to WormBase (M.A.T and T.S.) and NIH-ORIP (P40 OD010440) to the CGC (A.D.). The following individuals made substantial contributions to the C. elegans nomenclature system and its utilization: Sydney Brenner, Robert Horvitz, Jonathan Hodgkin, Robert Herman, Phil Anderson, Mark Edgley and Don Riddle.
Funders:
Funding AgencyGrant Number
NIHU41 HG002223D
NIHP40 OD010440
Record Number:CaltechAUTHORS:20180508-123432972
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20180508-123432972
Official Citation:Tuli M.A.,Daul A., Schedl T. Caenorhabditis nomenclature. (August 8, 2018), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.183.1, http://www.wormbook.org.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:86282
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:14 Jun 2018 17:34
Last Modified:04 Sep 2018 23:02

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