(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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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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