Gene nomenclature guidelines for the planarian Schmidtea mediterranea
We describe a gene nomenclature system for the freshwater planarian Schmidtea mediterranea. Guidelines are specified for designating names for genes and proteins, as well as for describing RNA-mediated genetic interference (RNAi) experiments. The proposed conventions aim to avoid multiple names being ascribed to single genes and to establish a uniform, simple method for naming genes in S. mediterranea that is readily understood by researchers working on planarians and other organisms. Developmental Dynamics 237:3099–3101, 2008. © 2008 Wiley-Liss, Inc.
Planarians are emerging as a powerful model for the study of numerous aspects of metazoan biology, including regeneration (Cebria et al.,2002; Reddien et al.,2005a; Gurley et al.,2008; Iglesias et al.,2008; Petersen and Reddien,2008), stem cells (Newmark and Sánchez Alvarado,2000; Reddien et al.,2005b; Salvetti et al.,2005; Oviedo and Levin,2007; Palakodeti et al.,2008), and tissue turnover (Pellettieri and Sánchez Alvarado,2007; Reddien et al.,2007). Because of the sequenced genome, extensive EST resources (Sánchez Alvarado et al.,2002; Zayas et al.,2005), and the ability to study gene function with RNAi (Sánchez Alvarado and Newmark,1999; Newmark et al.,2003), the community of researchers studying the planarian Schmidtea mediterranea is expanding rapidly. Therefore, a need exists to develop guidelines for naming S. mediterranea genes and proteins, such that the same molecule is not given multiple, alternate names. Lack of nomenclature standards would pose a challenge to the effective organization and exchange of biological information. Similar needs led in the past to the standardization of gene nomenclature of now-established model organisms such as mice (Davisson,1994), zebrafish (Mullins,1995), Caenorhabditis elegans (Horvitz et al.,1979), Drosophila melanogaster (Lindsley and Zimm,1992), Dictyostelium discoideum (Wood,1998), and yeast (Wood,1998), as well as humans (Wain et al.,2002). Here we provide suggested gene nomenclature guidelines that introduce a common format for the published discussion of genes from the planarian S. mediterranea. These general recommendations should be followed when possible, but will be extended and modified as further progress is made in the study of planarian genes.
SUMMARY OF GENE NAMING CONVENTIONS
Paralogous genes: Smed-genex-1 and Smed-genex-2
Double RNAi: Smed-genex(RNAi); Smed-geney(RNAi)
Short hand for RNAi of two paralogs: Smed-genex-1, -2(RNAi)
KEY FEATURES OF GENE NOMENCLATURE:
- 1The italicized prefix “Smed-” should be appended to all S. mediterranea gene names. After the gene name has been defined in a text, the prefix “Smed-” can be dropped to simplify use, except in those instances in which there may be some ambiguity about the species being discussed. When in doubt, the italicized “Smed-” prefix should be used when referring to the planarian gene.
- 2Gene names are listed in italics and lowercase (except the “S” in the “Smed-” prefix.) Proteins are listed in non-italics, all uppercase.
- 3Gene names should be selected to match the convention of a known homologous gene whenever possible. The intention is to make it as easy as possible to identify homology by the name. For example, a gene named Smed-genex would be a gene similar to the gene named “genex” in other species. When possible, gene names should try to match orthology. For example, if the S. mediterranea gene of interest is a clear ortholog to genex4 of a conserved genex gene family, the name for the planarian gene becomes Smed-genex4. When uncertain about orthology, simply indicating similarity is recommended (i.e., Smed-genex).
- 4When a planarian gene is similar to a gene typically described with an established acronym, the acronym can be used as the gene name. Note that it is appropriate in this instance for the case of the gene name to match the commonly used case of the acronym. For example, Smed-yfACRNM is a gene similar to a gene or class or genes typically described with the acronym “yfACRNM.” The gene name remains italicized. When in doubt, name the gene in all lowercase characters.
- 5If multiple genes of a particular class exist (e.g., paralogs), gene names have an appended number (not a letter), separated by a hyphen. For example, Smed-genex-1 and Smed-genex-2 would be two genex-like genes. If the gene is the only representative of a class, then no number is needed. For example, Smed-geney would be a geney-like gene for which a S. mediterranea gene family is not recognized. When in doubt, or when aware of an unpublished gene family, add a “-1” on the first gene named. In the event that a previously unknown paralog of a named gene (e.g., hypothetical Smed-geney) becomes recognized, the next gene is named with a “-2” (e.g., Smed-geney-2). In this event, the original name (e.g., Smed-geney) remains the same for the first gene.
- 6When genes encode a predicted protein that lacks clear sequence similarity to a previously named protein from another organism, genes can be named based upon an RNAi phenotype or expression pattern. In these cases the prefix “Smed” is not required. For example, a novel gene for which RNAi causes paralysis could be called “paralyzed.” If the gene is similar to a gene in another organism that has not been ascribed a descriptive name (e.g., the gene has only been ascribed a genome sequence or EST annotation), it is preferable to give the S. mediterranea gene a descriptive name of choice.
- 7When describing an RNAi experiment, the italicized notation “(RNAi)” is added: Smed-genex(RNAi). When describing an experiment involving multiple RNAi constructs, genes are separated with a semicolon: Smed-genex(RNAi); Smed-geney(RNAi). Shorthand for the RNAi of two paralogs can be used: Smed-genex-1, -2(RNAi) animals. As described above, after gene definition, the prefix “Smed-” can be dropped: genex(RNAi); geney(RNAi).
- 8For genes that have a very long name, a shorthand name can be ascribed in parentheses after defining the gene name. For example, Smed-verylongname would be a gene similar to the verylongname gene. As described above, this gene could be written “verylongname” after defining the gene in a text. As an alternative, a shorthand notation can be defined: e.g., Smed-verylongname (vln). In this example, the shorthand vln could then be used later in a text. Three letter notations are recommended where sensible, but shorter or longer notation may be appropriate on a case-by-case basis. Shorthand gene names are lowercase and in italics whereas shorthand protein names should be all uppercase and non-italics.
Because mutant alleles and transgenes are not yet commonly used in planarians, we have not provided nomenclature guidelines for describing such genetic modifications.
Gene naming nomenclature is summarized in the S. mediterranea genome database (SmedGD) at http://smedgd.neuro.utah.edu. Future changes and/or additions will be also posted at SmedGD. Queries on recommended nomenclature for S. mediterranea genes should be addressed to: firstname.lastname@example.org.
We thank Drs. Kyle Gurley and Christian Petersen for input on the development of these guidelines.