Gene and mutation nomenclature

[Hsinyugithub]

Just discussed this with Martin about naming of genes and mutants in PHI-base. I found the naming is not always consistent in the past. I remember the naming in Saccharomyces Genome Database (SGD) is quite logical and perhaps we can consider adapt the same Format (described below).That said, the community might find consistent naming a bit unusual. For instance, people tend to use 'Fg12' instead of 'FG12'. Please discuss, so we can determine the best way forward for PHI-base.

1. Standard Gene Names Format: Three uppercase letters followed by a number (e.g., ADE2, HIS3, GAL4).

2.Allele and Mutation Naming.
Wild-type allele: Same as the gene name (e.g., ADE2).
Mutant allele: Lowercase gene name with a number or descriptor (e.g., ade2-1, ade2Δ).
ade2-1: A specific point mutation.
ade2Δ: A deletion of the gene.

Below is an example of our entries:

[martin2urban]

There is also the paper by Yoder et al, 1985, Genetic Nomenclature and Practice for Plant Pathogenic Fungi, DOI: 10.1094/Phyto-76-383 - which recommends that for mutant alleles small letter should be used.

I made an example in Canto how this would look like for 'complementations':