Dictyostelium discoideum has a genome of approximately 34 Mb, containing approximately 12,500 genes. Thousands of mutant strains have been obtained, many of which are available from the Dicty Stock Center. A uniform nomenclature is essential to compile all the available information and provide easy access for the research community. We therefore encourage researchers to conform to the following guidelines for naming Dictyostelium genes, proteins, mutant alleles, strains, phenotypes, genotypes, plasmids, molecular genetic constructs, and chromosomes.
See the Procedure for naming genes for more details.
Questions and comments should be addressed to dictybase@northwestern.edu.
Dictyostelium gene names should be in lower case, italicized letters, followed, when necessary by a capital italicized letter or a number to distinguish genes sharing a prefix.
We strongly discourage using "D", "d", or "Dd" for Dictyostelium, and "g" and "p" for "gene" and "protein", as these abbreviations are not informative.
Strains are annotated with both a Systematic Strain Name and a Strain Descriptor.
gene-/[promoter]:gene(substitution or truncation):marker |
- | endogenous mutant allele (typically a null or a functional null mutant) |
/ | compound mutant |
[ ] | promoter gene |
( ) | indicates a substitution and/or a truncation |
: | represents a fusion between two genes |
[unk] | gene fusion to an unknown promoter |
[OE] | overexpressor under the control of an unspecified promoter |
[KD] | knockdown strain when the method is unknown |
[AS] | antisense strain |
[RNAi] | interference RNA strain |
[inviable] | precedes strains described as inviable |
dictyBase is using a vocabulary based on PATO (Phenotypic Quality Ontology) for phenotype annotations. Some documentation is available at this link. Phenotype terms are composed of two terms: an entity (biological process or anatomical structure abnormal in the mutant) and a quality that describes the abnormality. For example, a mutant that exhibits a delay in the aggregation process will be annotated to "delayed aggregation." The complete list of terms used to annotate Dictyostelium phenotypes can be viewed here. We encourage researchers to use this vocabulary in publications to ensure that genes get annotated accurately.
Genotypes represent the genetic modifications present in a given strain. Genes listed in a genotype are considered to be mutant in some way. Every genetic element described in a genotype (gene, plasmid, DNA fragment) should be separated by a comma. To distinguish chromosomal loci from exogenous genes, every gene or construct contained on DNA that was introduced into cells by transformation should be listed within brackets regardless of whether that DNA is carried on a plasmid, integrated as a fragment or was amplified by replication once inside cells.
Constructs carried within cells should be described in the formal genotype of that strain and placed in brackets. Thus, a cotB promoter beta-galactosidase reporter construct in a mutant strain might have a formal genotype of “regA(AK202), [cotB/lacZ], neoR”, but could be shortened to “regA-[cotB/lacZ]” in the context of a sentence describing the strain's properties in the results section of a paper.
The following names should be used to indicate common drug resistance/sensitivity and nutrient auxotrophy/prototrophy. For clarity, relevant phenotypic markers should be included at the end of formal genotypes (no italics):
Naturally occurring plasmids are named by a prefix indicating the genus and species, as in Ddp1. Derivatives of the natural plasmids and other shuttle vectors should be indicated with a lowercase “p” prefix (pDXA-3C). For genes on a plasmid, and any other gene that is introduced into a strain by experiment (see below), use the same naming system as for chromosomal genes, but placed within square brackets.
Example: pDneo67[act6/regA] indicates that the regA coding sequence is fused to the promoter of the actin6 gene on plasmid pDneo67).
Reporter genes and gene fusions should be named with the relevant components separated by slashes and dashes to indicate DNA fusion, as follows. Typically, the components will be a promoter, a coding sequence or ORF encoding a reporter protein. Promoters (± a few codons) should be separated from coding sequence by a slash (/) and coding sequences separated by dashes (-).
Examples: cotB/talA-GFP (talin-GFP fusion under the transcriptional control of the cotB promoter), talA/talA-GFP or talA-GFP (talin gene under the transcriptional control of the native promoter), talA-GFP(S65T).
Chromosomes are designated by non-italic Arabic numbers.
Example: Chromosome 1.
dictyBase acts as the centralized clearinghouse for gene and strain names. Scientific curators at dictyBase will verify proposed gene and strain names to encourage the application of these guidelines and to ensure that names are not duplicated. Questions or naming suggestions can be addressed to: dictybase@northwestern.edu.
This document is based on the Nomenclature Proposal written in November 2000 by the Dictyostelium Community Organizing Committee: Adam Kuspa (Chairman), Robert R. Kay, Alan R. Kimmel, Hideko Urushihara, Richard Kessin (ex officio) Chairman.
General:
Demerec, M. et al., (1966). A proposal for a uniform nomenclature in bacterial genetics. Genetics 54:61-76.
Kay, Loomis, Devreotes (2001) TIG S.5-S.6
Gene Names List: Dictyostelium discoideum gene list at dictyBase
AD, HAD | Adrian Harwood |
AK | Adam Kuspa |
ARK | Alan Kimmel |
AJW | Alan Warren |
BS | Bubba Singleton |
BW | Bin Wang (Kuspa lab) |
CT | Chris Thompson |
CW | Tom Egelhoff |
DG | Bill Loomis (Developmental Gene) |
DH | Dale Herald (except DH100-199: Rich Kessin) |
DR | Doug Robinson |
GS | Gad Shaulsky |
HAD | Adrian Harwood |
HC, DCB | Barrie Coukell |
HDK, DDK | David Knecht |
HDT | Meg Titus |
HG, DG | Guenther Gerisch |
HGR | Michel Sartre |
HH, DH100-199 | Rich Kessin (Haploid Harvard) |
HJW, JGW | Jeff Williams |
HK, DK | Gene Katz |
HKT | Kei Inouye |
HL, DL | Bill Loomis |
HM, DM | Rob Kay |
HMW | Randy Dimond (Haploid Madison Wisconsin) |
HO | Terry O'Halloran |
HP, HPX | Pasteur Institute |
HPF, DPF | Paul Fisher |
HPS, DPS | Reg Deering (Haploid Penn State) |
HR | Herb Ennis and Rich Kessin (a few strains from Frank Rothman were labeled HR too) |
HS, DS | Jim Spudich |
HSB | Salvo Bozzaro |
HT | Adrian Tsang |
HTU | Taro Uyeda |
HTY | Kaichiro Yanagisawa |
HU, DUK | Keith Williams |
HUD, DUD | Dennis Welker |
HW | Chris West |
IIB | Instituto de Investigaciones Biomedicas |
IR, DIR, RI (old) | Rob Insall |
JB | Jane Borleis (Peter Devreotes' lab) |
JGW, HJW | Jeff Williams |
JH | Jeff Hadwiger |
JM | Jacqueline Milne (Peter Devreotes' lab) |
JS | Justin Stege (Bill Loomis' lab) |
KS | Karl Saxe |
KY | Kaichiro Yanagisawa (or T. Yamada?) |
LW | Lijun Wu (Peter Devreotes' lab) |
NP, DP | Peter Newell |
PD | Peter Devreotes |
QS | Queller-Strassmann lab |
RI | Rob Insall (old prefix) |
SA, DSA | Steve Alexander |
SB | Simone Blagg |
TL | Bill Loomis |
V | Adam Kuspa |
W | Adam Kuspa |
WTC | Wen-Tsan Chang |
X, XP | Peter Newell |
XMC | Hideko Urushihara (XP55-derived MaCrocyst defective) |
Updated on September 4, 2009