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Nomenclature and Terminology

Nomenclature and Terminology

Molecular Plant 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 standard common name at first use if such exists, with the scientific name in parentheses. Subsequent references to organisms can be either scientific 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 state

Authors are responsible for determining that all nomenclature conforms to accepted community standards prior to submission. Some helpful resources follow, including nomenclature guidelines for the taxa of several research communities. (Okay, Zack)

http://www.arabidopsis.org/portals/nomenclature/guidelines.jsp (Arabidopsis)
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 refer

Authors should be aware that nomenclature conventions differ among species and so, for instance, Arabidopsis nomenclature should not be used for other species, or vice versa, because the symbol may have already been used for another purpose in the second species. 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 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).

Relationships between homologous genes. Molecular Plant follows the recommendations of Theissen (Nature 415:741, 2002) and Fitch (Trends in Genetics 16:227-231, 2000) for usage of terms that describe relationships between genes. Homology is a relationship between features or genes that share a common evolutionary origin. DNA sequences may be homologous or not, but they may not be "partially" or "highly homologous"; percent sequence similarity may be used, but not "percent homology." Paralogy is a relationship between genes that have originated by gene duplication, whereas orthology is a relationship between genes that originated by speciation. If orthology or paralogy have not been established by a proper phylogenetic analysis, "homolog(ue)" or modified terms such as "putative ortholog(ue)" or "likely paralog(ue)" should be used. Homeolog(ue) is preferred over paralog when gene pairs have arisen via polyploidy as opposed to gene or segmental duplication.

Gene fusions and constructs. Gene fusions may be indicated by either a single colon or a hyphen, but not by a double colon. For example, 35S:GFP, 35S-GFP, CRY2:GFP, and CRY2-GFP are acceptable to refer to promoter-coding sequence fusions and fusions of coding sequences. A double colon should be used only for insertions (such as insertions by transposable elements), as in An1::dTph1, Bz1::Ac, or LFY::TAG1. Lowercase "p" should be used to refer to plasmids (e.g., pBR322), and to avoid confusion it should not be used to refer to promoters. Authors should designate promoters as, e.g., P35S, Pro35S, or 35Spro and promoter/coding sequence fusions as P35S:LFY, Pro35S:LFY or 35Spro:LFY. Transactivations should be written, e.g., PFIL>> or FILpro>>.

Genes and mutations. The standard definition of the term gene in molecular terms is the complete segment of chromosome that is required for expression of a gene product (i.e., including promoters, enhancers, introns, exons, untranslated regions, etc.) Thus, a coding sequence or transcription unit should not be referred to as a gene, but rather as a component of a gene. To avoid confusion, double or triple mutations should contain the names of the mutated genes separated by a space, e.g., sad1 sad2, or cad4 cad5 cad 6 and should not be given entirely new names.

Authors should note that insertional mutations are not necessarily "knockout" mutations and should not be referred to as such unless they have been shown experimentally to be null alleles. Also, putative insertional mutations should generally be characterized at both ends of an insertion prior to manuscript submission; otherwise, the possibility cannot be ruled out that the observed sequence fusion represents a translocation rather than an insertion.
Generally, characterization of multiple, independent alleles is necessary to establish that a mutation (such as a T-DNA insertion or chemically induced mutation) is responsible for an observed phenotype, as opposed to an undetected, linked mutation. Complementation tests via transformation can be valuable, although their interpretation may be limited by the possibility of redundancy, and so statements of proof should be limited to cases in which multiple independent alleles have been characterized.