Gene Naming Guideline

Open Access Publication | Detailed Guideline | Gene Class Symbol | Species Prefix

Gene Naming Guidlines

Genes in GDR are composed of two types:

1. Genes with gene symbol, assigned by individual investigators, usually with known or predicted function or phenotype.
   • These genes with gene symbols in GDR are obtained by parsing the NCBI nr database and submission from individual investigators.
   • Prior to naming your genes, please refer to the list of gene class symbols in Rosaceae and gene naming guidelines below and submit the gene/gene class data.
2. ​Genes predicted from the whole genome assembly

1. Naming Guideline for Genes with known or predicted function or phenotype

(for gene data submission and gene nomenclature in manuscript)

The guideline has been put together by Rosaceae Gene Name Standardization Subcommittee of RosEXEC/RosIGI.

Gene Symbol is composed of:

[species prefix][3-letter code class symbol].[numeric suffix for a gene][-|_][numeric suffix for an allele or a splice variant]

Where

• [species prefix]: publication purposes - three letter prefix for major species and 5 letter prefix for others
• [3-letter code class symbol]: a 3 letter class symbol for closely related genes
• [numeric suffix for a gene]: numeric suffix for a gene. the gene symbols do not contain a number, a numeric suffix can be directly attached without the proceeding period.
• [-|_]: publication purposes a hypen for alleles  and an underscore for splice variants
• [numeric suffix for an allele or a splice variant]

Examples:

• When the gene symbols do not contain a number: PG1, PG2
• When the gene symbols do contain a number: DHN3.1, DHN3.2
• alleles: DHN3.1-1, DHN3.1-2
• splice variants: DHN3.1_1, DHN3.1_2
• to compare genes from multiple species: PpeDHN3.1, MdoDHN3.1

Please refer to the page for detailed guideline.

2. Naming Guideline for Predicted Genes from Whole Genome Assembly