The Zebrafish Book
CHAPTER 7 - GENETIC METHODS
Conventions for Naming Zebrafish Genes
(Source: M. Mullins)
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. A summary of current nomenclature
guidelines is available on ZFIN.
Naming genes identified by mutation
1. The name of a gene identified by mutation should refer to the ostensible phenotype of the mutant without any
inherent interpretation of the phenotype. It should not be too specific. Determining the molecular mechanism by
which a phenotype is produced can be a formidable task and should not be inferred by the name of the gene. The
name should be a mnemonic for the mutant phenotype. For example, cyclops is an excellent name for the
mutation isolated in Eugene that produces a cyclopic phenotype.
2. The name should be unique, one or two words, and italicized. Longer names tend to be impractical to use.
Avoid choosing names identical to those used in other species.
3. For mutations in different genes that all have similar phenotypes, a single name followed by consecutive
numbers should not be used. This nomenclature makes the field less accessible to the outsider. A mutation in
a second gene resulting in cyclopia could be called fused-eyes, but should not be called
cyclops2.
Naming cloned genes
1. For nonhomologous "novel" genes identified by cloning, the conventions above apply with the exception of the
use of numbers. For a new gene family, it would be appropriate to name the individual genes in the family with a
single family name followed by consecutive numbers. The numbers would immediately follow the name with no hyphen
or space between them. No further letters would follow this number in the gene name. For example, abc1,
abc2, abc3 are appropriate; however, abc1A, abc1B, and abc1C are
inappropriate.
2. For homologous genes cloned (rather than those with just some sequence similarity which are probably not
true homologues), the same name as in the counterpart organism should be given to the zebrafish gene. This
would make it easier to follow "homologue" work in different organisms. The fish gene should not be preceded
with "Z" or "Zf", otherwise there will be thousands of zebrafish genes beginning with "Z....". For example,
a zebrafish homologue to the mouse Wnt1 gene becomes the zebrafish wnt1 gene.
Abbreviated name
A gene identified either by mutation or molecular analysis should be abbreviated by three lower case italicized
letters or by three lower case letters and a number (no hyphen) italicized. All letters should be roman, i.e. no
greek letters. The letters should be unique with respect to other named zebrafish mutants and genes and should
be letters derived from the full name. For example, the abbreviated name for cyclops is cyc.
Numbers should generally not be used in naming a gene identified only by mutation. When a number is included in
the name (see Naming cloned genes, above), there should be no hyphen or space between the letters and the
number. Genes identfied as homologues to human or mouse genes should use the same abbreviation, if possible, and
thus are not limited to 3 letters.
Alleles
The allele-specific designation should be denoted by a superscript. Dominant mutations will be designated by "d"
in the first position of the superscript. All allele names without a "d" then indicate a recessive allele. The
next position of the superscript (this will be the first position if the mutation is recessive) will be a lower
case letter that designates the laboratory in which the mutation was isolated. This laboratory letter is then
followed by unique numbers and/or letter(s) for the particular allele which completes the allele designation.
Because "d" will denote "dominant", "d" cannot be used for a laboratory designation. Each allele designation
from a given laboratory is unique. Because each laboratory has a different letter designation, all mutant
alleles from all zebrafish laboratories are unique and can be accessed easily by computer. ZFIN maintains a list of laboratory allele designations. You can contact ZFIN to obtain an allele designation.
For example, in Eugene all allele names begin with "b" and are numbered sequentially, approximately in the
order they were recovered. cycb16 is an allele of cyclops that was isolated in
Eugene (b). b16 is a unique allele designation in Eugene. No other mutant allele in Eugene or
elsewhere will have this allele designation whether it be cyclops, spadetail, golden,
etc.
Priority in names
1. When mutations in the same gene are found independently in more than one laboratory and given different
names, then the name that appears first in the literature will be given priority. Sometimes different mutant
alleles of the same gene can have very different phenotypes and it may take a while before it is shown that the
mutations are in the same gene. The first published name would get priority and all other alleles would adopt
this designation.
2. When a mutation is found in a previously cloned zebrafish gene (which has been published), then the mutant
will take the cloned gene's name. For example, in Monte Westerfield's laboratory a mutation was induced in
the msxb gene. The mutation in the gene is also be referred to as msxb (in this case,
Dfmsxb,
because the mutation is a deficiency).
3. If both the cloned gene and the mutation already exist with different names and at some later point they
are found to be the same gene, then the name of the mutation takes priority even if the cloned gene was
named first. In this case the unique name of the mutation would probably be more relevant to the function of
the gene than the cloned gene's name, and this unique mutant name would be easier to remember than the gene
name. If in the example above, a mutant named braindead (bdd) had been characterized, and it
was later discovered to be a mutation in the msxb gene, then the msxb gene would now be
designated bdd.
With these conventions, some changes have already been made in mutant designations. Two previously
identified recessive pigmentation mutants golden1 and golden2 contain mutations in two
different genes. Charline Walker and Chuck Kimmel decided to change the name of golden2 to
brass (brs) and golden1 to just golden (gol). This should avoid any
future confusion about golden2 being a second allele of golden.
An unsettled issue
In the case of zebrafish homologues where the nomenclature in the counterpart organism is contrary to our
nomenclature, there is still no convention. The two schools of thought can be illustrated through the naming of
the zebrafish homologue to the mouse Brachyury gene, abbreviated as T.
One nomenclature puts the importance of a common nomenclature between organisms above that of the
nomenclature within zebrafish. In this case the zebrafish homologue of the mouse T gene would also be
named T in zebrafish. As discussed above, it would be against our conventions to capitalize the gene
name and to use only one letter, however, since in mouse the abbreviated name is capitalized we would now
capitalize the name in zebrafish.
A second nomenclature puts the importance of the zebrafish nomenclature above that of a nomenclature common
among organisms. In this case, the zebrafish homologue to the mouse Brachyury or T gene could
be named brachyury and abbreviated in zebrafish as bry to follow our nomenclature. This
example is further complicated because the zebrafish homologue of the Brachyury mutant has been shown
to be no tail (ntl). The zebrafish convention would be to call this mutant no tail
whereas as the other convention would rename it brachyuria.
The
Zebrafish Book
