[Arabidopsis] gene names in different species?

Nan Eckardt via arab-gen%40net.bio.net (by neckardt from aspb.org)
Fri Oct 26 16:49:11 EST 2007

Hi Colleen,
You might find the information from The Plant Cell Instructions for
Authors helpful (posted online at http://www.plantcell.org/). They are
good general guidelines.
Nan Eckardt
Nancy A. Eckardt, Ph.D.
News and Reviews Editor
THE PLANT CELL www.plantcell.org
Home office:
1503 Woodrose Ct.
Fort Collins, CO 80526
Phone/fax: 970-495-9918
neckardt from aspb.org

Nomenclature and Terminology. The Plant Cell requires that all
nomenclature, including gene names and symbols, conform to nomenclature
conventions adopted by the scientific community and that all genetic
terminology be used in a scientifically accurate manner. 

     Organisms. In the Abstract, text, and Methods, organisms should be
referred to by their common name at first use (if a standard common name
applies), and the Latin name should be given in parentheses. Subsequent
references to organisms can be either Latin or common names but should
be consistent throughout the manuscript.

     Gene and protein symbols. Prior to submission, authors should
determine that all gene and protein symbols used in a manuscript have
priority in the literature. When introducing new symbols, the manuscript
cover letter must state that the authors have conducted a search of the
literature and of relevant community databases and that the new symbol
has priority and has been registered in the appropriate community
database (if one is available for the species in question). New gene
symbols should be compliant with the naming conventions of the relevant
research community. Priority may be established for a gene symbol either
by publication in the literature or formal registration in a community
gene symbol database. Possible conflicts and/or confusion regarding
nomenclature should be resolved prior to submission, if possible, and/or
addressed in the cover letter. The full name for a gene should be stated
where first used in the manuscript. Full gene names, not symbols, should
generally be used in the title of the manuscript.

Authors are responsible for determining that all nomenclature conforms
to accepted community standards prior to submission. Some helpful
resources follow.

http://www.maizegdb.org/maize_nomenclature.php (Maize) 
http://www.gramene.org/newsletters/rice_genetics/rgn3/v3C.html (Rice)
Nomenclature rules are being revised by the rice community at this time.
When a new link is available, it will appear here.
http://wheat.pw.usda.gov/ggpages/wgc/98/ (Wheat) 
http://tgrc.ucdavis.edu (Tomato) 
http://www.chlamy.org/nomenclature.html (Chlamydomonas) 
VandenBosch, A., and Frugoli, J. 2001. Guidelines for genetic
nomenclature and community governance for the model legume Medicago
trunculata. MPMI 14, 1364-1367.
http://www.chem.qmw.ac.uk/iupac/ (protein nomenclature) 
http://www.expasy.org/cgi-bin/lists?nomlist.txt (list of
nomenclature-related references for proteins) 

Nomenclature conventions differ among species and so, for instance,
Arabidopsis nomenclature should not be used for other species, or vice
versa. Note also the requirements for case: nearly all plant species use
uppercase for the first letter and lowercase for subsequent letters,
whereas all letters are uppercase in Arabiodopsis and Petunia genes and
proteins. Maize genes are referred to with only lowercase letters,
except when referring to dominant alleles. Prefixes indicating species
(e.g., At, Zm, Os) are not generally allowed as part of a gene symbol,
except to avoid confusion in cross-species comparisons. Where used, a
two-letter prefix (e.g., At for Arabidopsis thaliana) should not be
italicized as it is not part of the gene symbol and should be separated
from the gene name by a space or hyphen. Although a lowercase "p" is
used to indicate the protein product of a gene in Saccharomyces
cerevisiae nomenclature (e.g., SNF2p), this is not used in most plant
nomenclature systems; please use the accepted protein nomenclature
system for the species in question. 

Symbols for putative orthologs often differ between species. However, if
probable orthology has not been established, genes should not be named
or renamed for homologs in other species because this may create
confusion in the future when more gene sequences are known in the
species and true orthologs can be predicted with greater confidence.
Authors may propose a revised nomenclature for a given clade of
orthologs using a shared symbol (e.g., Xyz1), accompanied by two-letter
prefixes (e.g., Zm, At, Hv, etc.; defined in the Methods and not
italicized) to indicate species: e.g., Zm Xyz1 and Os Xyz1. All such
proposals must be based on good phylogenetic information demonstrating
probable orthology (see definition below). 


Nancy A. Eckardt, Ph.D.
News and Reviews Editor
THE PLANT CELL www.plantcell.org
Home office:
1503 Woodrose Ct.
Fort Collins, CO 80526
Phone/fax: 970-495-9918
neckardt from aspb.org

-----Original Message-----
From: arab-gen-bounces from oat.bio.indiana.edu
[mailto:arab-gen-bounces from oat.bio.indiana.edu] On Behalf Of
Colleen.MacMillan from ensisjv.com
Sent: Friday, October 26, 2007 2:31 AM
To: arab-gen from magpie.bio.indiana.edu
Subject: [Arabidopsis] gene names in different species?


Does anyone have info on what rules might have been suggested for naming
of genes in different species?  If for example a gene has been named in
one species, should phylogenetically related genes in other species be
named after the original gene-name?  Or, is it the norm to name genes in
each species at the discretion of the people who clone it?  

Yes of course "a rose by any other name ..." but I thought might be good
to check whether a system of gene-naming exists.




Dr Colleen MacMillan

CSIRO Forestry (Ensis Genetics)

phone: +61-02-62818361

post: POBox E4008, Kingston, ACT 2604, Australia

location: Building 1, Wilf Crane Crescent, Yarralumla, ACT, Australia


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