(Source: The Zebrafish Nomenclature Committee from Zebrafish Book 5th Edition)
Genetic designations vary immensely from organism to organism, and the zebrafish community recognizes the importance of agreeing upon conventions for naming mutants and genes. The following conventions have been chosen by most labs to minimize confusion and maximize the utility of the nomenclature and the ease with which people outside (as well as those within) the field can follow the field. It is very important that the entire zebrafish community adopt one set of conventions. The current nomenclature guidelines are available from ZFIN.
Contents
1. Gene names and symbols
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7. Contributors
8. References
1. GENE NAMES AND SYMBOLS
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Gene names should be registered at httphttps://zfin.org/cgi-bin/webdriver?MIval=aa-new_gene.apghttp://zfin.org/cgi-bin/webdriver?MIval=aa-new_gene.apgaction/nomenclature/gene-name
1.1 Genes identified by cloning Genes should be named after the mammalian orthologue whenever possible. When mammalian orthologues are known, the same name and abbreviation should be used, except all letters are italicized and lower case. Members of a gene family are sequentially numbered.
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Mutant names should be registered at httphttps://zfin.org/action/cgi-bin/webdriver?MIval=aa-new_line.apghttp://zfin.org/cgi-bin/webdriver?MIval=aa-new_line.apgnomenclature/line-name.
1.4 Genes identified only by genomic sequencing projects
Large-scale genome sequencing projects use a variety of prediction methods to identify both open reading frames and genes. Some of these genes are already known, while others are new. Novel genes identified by these means often cannot be identified and are assigned a name comprised of a prefix, a clone name, and an integer. The prefix is used to specify the research institution that identified the gene (e.g., "si" for the Sanger Institute). A colon separates the prefix from the clone identifier. In many cases, there are multiple predicted reading frames in a single clone. These genes are distinguished with a full stop (period) between the clone name and an integer. Integers are assigned to genes in the clone as they are identified and do not indicate the order of genes. If part of a gene is found in more than one clone, the name of the first clone in which the 5' portion of the gene is found takes precedence.
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b is the Eugene designation; m is for MGH, Boston; t is Tuebingen, Germany
wild type_: lof{}{},_ ndr2, brs+ mutant: lofdt2, ndr2b16, ndr2m101, ndr2t219
3.2 Genotype nomenclature for publications
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{abcb000defm000{color:lack}} (poorly resolved loci on same chromosome)ednrb1b140 {abcb000defm000{color:lack}} cx41.8t1 (poorly resolved loci in a known interval between mapped loci, all on same chromosome)
3.3 Genotype display at ZFIN
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Due to technical constraints, genotypes at ZFIN are shown in alphabetical order by gene, and then by allele designation. See below for display of complex genotypes involving transgenic or chromosomal rearrangements.
4. CHROMOSOMES AND ABERRATIONS
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Example: Tg(-0.7her5:EGFP)ne2067;hmgcrbs617/s617
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5. PRIORITY IN NAMES
As described above, zebrafish genes are named based on orthology to a human or mouse gene. If an ortholog cannot be identified, then the name that appears first in the literature will be given priority assuming it follows other nomenclature guidelines. ZFIN recommends submission of proposed gene names via the ZFIN form or consultation with the zebrafish nomenclature committee (nomenclature@zfin.org) for nomenclature assignment.
When a mutation is found in a previously cloned zebrafish gene, then the mutant will be referred to as an allele of the gene. If both the cloned gene and the mutation are known by different names and later found to be the same gene, then the name of the gene usually takes priority. The exception to this rule is when the mammalian gene has a gene symbol that is less than two characters such as the mouse gene brachyury which has the symbol T. In this case the zebrafish gene retained the original name no tail, ntl.
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6. MAPPING AND SEQUENCING INFORMATION
The genome project began in 1994, and by 1996 the genetic map was closed. NIH funded major programs to develop a doubled haploid meiotic mapping panel, deficiency strains and expressed sequence tags (ESTs), The ESTs and anonymous markers have been mapped on two radiation-hybrid panels. The Sanger Institutebegan full genome squencing in 2001. A physical map is being constructed from the BAC libraries used for sequencing. Genomic information is updated regularly on ZFIN.
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7. CONTRIBUTORS
Marc Ekker (marc.ekker@science.uottawa.ca), Center for Advanced Research in Environmental Genomics, University of Ottawa, Ontario, Canada
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