Final Nomenclature Decision

BTNYDWM at MVS.UCC.OKSTATE.EDU BTNYDWM at MVS.UCC.OKSTATE.EDU
Fri Oct 1 10:49:00 EST 1993


To Members of the Arabidopsis Community:

Several weeks ago I raised the question of nomenclature in
Arabidopsis with particular reference to dominant mutations.
A considerable amount of discussion followed over this email
network.  I then summarized the responses as part of a final
recommendation to both the National (US) and Multinational
Arabidopsis Steering Committees.  I received responses from
everyone in the National committee and some members of the
Multinational committee.  Everyone who responded supported
my recommendation.  I then prepared updated nomenclature
guidelines for genes identified by mutations in Arabidopsis.
These formal guidelines are noted below.  Please make a copy
of these guidelines for your laboratory.  This information
will soon be sent to editorial offices of all major journals
to ensure some degree of quality control in gene nomenclature.

The issue of dominant mutations is covered in sections
I-I through I-L.  Please read these sections carefully.
There was no way to design a system that satisfied all
of the concerns raised in the recent email discussion.
I appreciate all of the suggestions and concerns raised
in that discussion, and hope that you will conform with
the community decision even if the results are inconsistent
with your own views.

Sincerely,

David Meinke
Curator of Mutant Gene Symbols

Nomenclature for Genes Identified by Mutations in Arabidopsis thaliana

I.  Specific Guidelines:

A.  Mutant gene symbols should have 3 letters (underlined or italics) in
    lower case.

B.  Some well-known symbols chosen before these guidelines were established
    may have only 2 letters.

C.  The wild-type allele should have these letters (underlined or italics)
    in CAPS.

D.  Protein products of genes should be in CAPS only.

E.  Phenotypes are designated by the gene symbol (no underline) with the
    first letter capitalized (for example: Abc+ wild type; Abc- mutant).
    The +/- can be superscript or on the same line.

F.  Different genes with the same symbol are distinguished by different
    numbers (abc1 and abc2).

G.  Different alleles of the same gene are distinguished with a number
    following a hyphen (abc4-1 and abc4-2).

H.  When only a single allele is known, the hyphen (-1) is not needed.
    Thus abc3 = abc3-1 if only a single allele is known.

I.  The same rules of nomenclature outlined above apply to both dominant
    and recessive mutations.  The community has discussed this particular
    feature of nomenclature at length.  Several modifications noted below
    were recently adopted.  Other methods of designating dominant alleles
    (CAPS, superscripts, etc.) should be avoided and will not be accepted
    into the Arabidopsis databases.

J.  Individuals may choose to add a "D" at the end of an allele number
    for purposes of outlining crosses if that allele exhibits simple
    dominance relative to wild type.  Thus abc5-2D indicates that allele
    #2 is dominant to wild type.

K.  A formal list of additional modifiers will be prepared as the need
    becomes apparent.

L.  Incorporation of these letters into the formal allele name maintained
    in databases is discouraged because such modifiers may be misleading
    in the absence of information on reference alleles.  Since this
    designation is optional, it should be noted that some dominant alleles
    will not have a "D" suffix.

M.  A copy of these guidelines for nomenclature in Arabidopsis will be
    distributed to editorial offices of major journals to help maintain
    this system in publications.

II. General Guidelines:

A.  Mutants should be characterized in some detail before a formal gene
    symbol is chosen and published.  This analysis should include (when
    possible) mapping the chromosomal location of the mutant locus.

B.  Complementation tests should be performed with mutants that map to
    similar regions and/or exhibit similar phenotypes to ensure that your
    mutant has not already been identified and assigned a different name.

C.  Avoid the use of symbols that have another meaning for biologists.

D.  Current lists of mutant gene symbols in Arabidopsis are available
    through stock centers and databases.  Consult these lists before
    selecting a formal gene symbol.

E.  Contact the curator of mutant gene symbols before publication to reserve
    your name and symbol of interest.

F.  The present curator is: David Meinke (Department of Botany, Oklahoma
    State University, Stillwater, OK 74078 USA; FAX 405-744-7673; email:
    btnydwm at mvs.ucc.okstate.edu).

Updated September, 1993






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