Genetic nomenclature - MetabolicEngineeringGroupCBMA/MetabolicEngineeringGroupCBMA.github.io GitHub Wiki

From Sherman, Fred. 2002. “Getting Started with Yeast.” Methods in Enzymology 350: 3–41.

Gene symbol	Definition
ARG+	All wild-type alleles controlling arginine requirement
ARG2	Locus or dominant allele
arg2	Locus or recessive allele conferring an arginine requirement
arg2-	Any arg2 allele conferring an arginine requirement
ARG2+	Wild-type allele
arg2-9	Specific allele or mutation
Arg+	Strain not requiring arginine
Arg-	Strain requiring arginine
Arg2p	Protein encoded by ARG2
Arg2 protein	Protein encoded by ARG2
ARG2 mRNA	mRNA transcribed from ARG2
arg2-∆1	Specific complete or partial deletion of ARG2
ARG2::LEU2	Insertion of the functional LEU2 gene at the ARG2 locus; ARG2 remains functional and dominant
arg2::LEU2	Insertion of the functional LEU2 gene at the ARG2 locus; arg2 is or became nonfunctional
arg2::KanMX4	Insertion of the functional KanMX4 gene at the ARG2 locus; arg2 is or became nonfunctional
arg2-10::LEU2	Insertion of the functional LEU2 gene at the ARG2 locus, and the specified arg2-10 allele which is nonfunctional
cyc1-arg2	Fusion between the CYC1 and ARG2 genes, where both are nonfunctional
PCYC1-ARG2	Fusion between the CYC1 promoter and ARG2, where the ARG2 gene is functional

The accepted genetic nomenclature for chromosomal genes of the yeast S. cerevisiae is illustrated in the table above, using ARG2 as an example.

Whenever possible, each gene, allele, or locus is designated by three italicized letters, e.g., ARG, which is usually a describer of the function, followed by a number, e.g., ARG2.

Unlike most other systems of genetic nomenclature, dominant alleles are denoted by using UPPERCASE italics for all letters of the gene symbol, e.g., ARG2, whereas lowercase letters denote the recessive allele, e.g., the auxotrophic marker arg2. Wild-type genes are designated with a superscript "plus" (sup6⁺ or ARG2⁺).

Alleles are designated by a number separated from the locus number by a hyphen (-), e.g., arg2-9.

The symbol ∆ (greek capital letter delta) can denote complete or partial deletions, e.g., arg2-∆1. (Do not use the symbols ∆arg2 or arg2∆ for deletions.)

Insertion of genes follow the bacterial nomenclature by using the symbol ::. For example, arg2::LEU2 denotes the insertion of the LEU2 gene at the ARG2 locus in which LEU2 is dominant (and functional) and arg2 is recessive (and defective).

Phenotypes are denoted by cognate symbols in roman type and by the superscripts + and -. For example, the independence and requirement for arginine can be denoted by Arg⁺ and Arg^-, respectively.

Proteins encoded by ARG2, for example, can be denoted Arg2p, or simply Arg2 protein. However, gene symbols are generally used as adjectives for other nouns, for example, ARG2 mRNA or ARG2 strains. Resistance and sensitivity phenotypes are designated by superscript R and S, respectively. For example, resistance and sensitivity to canavanine sulfate are designated Can^R and Can^S, respectively.

Although most alleles can be unambiguously assigned as dominant or recessive by examining the phenotype of the heterozygous diploid crosses, dominant and recessive traits are defined only with pairs, and a single allele can be both dominant and recessive. For example, because the alleles CYC1+ , cyc1-717, and cyc1-∆1 produce, respectively, 100%, 5 %, and 0% of the gene product, the cyc1-717 allele can be considered recessive in the cyc1-717/CYC1+ cross and dominant in the CYC1-717/cyc1-∆1 cross. Thus, it is less confusing to denote all mutant alleles by lowercase letters, especially when considering a series of mutations having a range of activities.

Auxiliary gene symbols can be used to further describe the corresponding phenotypes, including the use of superscript R and S to distinguish genes conferring resistance and sensitivity, respectively. For example, the genes controlling resistance to canavanine sulfate (can1) and copper sulfate (CUP1) and their sensitive alleles could be denoted, respectively, as can^R1, CUP^R1, CAN^S1, and cup^S1.