Revised fission yeast gene and allele nomenclature guidelines for machine readability

Abstract

Standardized nomenclature for genes, gene products, and isoforms is crucial to prevent ambiguity and enable clear communication of scientific data, facilitating efficient biocuration and data sharing. Standardized genotype nomenclature, which describes alleles present in a specific strain that differ from those in the wild-type reference strain, is equally essential to maximize research impact and ensure that results linking genotypes to phenotypes are Findable, Accessible, Interoperable, and Reusable (FAIR). In this publication, we extend the fission yeast clade gene nomenclature guidelines to support the curation efforts at PomBase (www.pombase.org), the Schizosaccharomyces pombe Model Organism Database. This update introduces nomenclature guidelines for noncoding RNA genes, following those set forth by the Human Genome Organisation Gene Nomenclature Committee. Additionally, we provide a significant update to the allele and genotype nomenclature guidelines originally published in 1987, to standardize the diverse range of genetic modifications enabled by the fission yeast genetic toolbox. These updated guidelines reflect a community consensus between numerous fission yeast researchers. Adoption of these rules will improve consistency in gene and genotype nomenclature, and facilitate machine-readability and automated entity recognition of fission yeast genes and alleles in publications or datasets. In conclusion, our updated guidelines provide a valuable resource for the fission yeast research community, promoting consistency, clarity, and FAIRness in genetic data sharing and interpretation.

Keywords: FAIR; allele; database; fission yeast; gene variant; genotype; knowledge base; model organism; nomenclature; standardization.

Fig. 1.

Graphical representation of representative alleles and their corresponding nomenclature. a) Alleles present in the ura4 locus and their corresponding names. In order: (1) The wild-type locus; (2) A deletion of the ORF without replacement (e.g. scar-free CRISPR-Cas9); (3) A deletion allele in which the ura4 locus was replaced by a KanMX6 cassette. Note that the deletion allele ura4Δ is used both to indicate the locus of insertion and the fact that the ura4 ORF is missing; (4) This allele name can represent the insertion of P.act1-GFP-ase1 at either side of the ura4 locus since the transcription orientation is not captured in the allele name; (5) For the same reason, a construct containing 2 flanking ura4 alleles can have 2 synonymous names when inserted in the ura4 locus; (6) Allele names should capture the insertion locus and the relative position of features, rather than how alleles were generated or their genetic meaning. Therefore, in a case where an allele of the insertion locus (ura4+ allele in the image) is in the middle of the construct, we use ura4Δ:: to indicate the insertion locus, followed by the construct name, including the ura4+ allele. b) Special cases in which an allele name contains 2 gene symbols (ase1 and ura4), and one of them is also the locus of insertion. The wild type locus is shown on top, and the resulting alleles and their names at the bottom: (left) If inserted in the ura4 locus replacing the ura4 ORF, the allele name starts with “ura4Δ::”; (center) If inserted in the ura4 locus keeping the ura4 ORF, the allele name starts with “ura4+::”; (right) If inserted in the ase1 locus, the allele name starts with “ase1-GFP::”.