Gephebase, a database of genotype-phenotype relationships for natural and domesticated variation in Eukaryotes.

Virginie Courtier-Orgogozo,Stéphane R Prigent,Arnaud Martin,Laurent Arnoult,Séverine Wiltgen

doi:10.1093/nar/gkz796

Abstract

Gephebase is a manually-curated database compiling our accumulated knowledge of the genes and mutations that underlie natural, domesticated and experimental phenotypic variation in all Eukaryotes—mostly animals, plants and yeasts. Gephebase aims to compile studies where the genotype–phenotype association (based on linkage mapping, association mapping or a candidate gene approach) is relatively well supported. Human clinical traits and aberrant mutant phenotypes in laboratory organisms are not included and can be found in other databases (e.g. OMIM, OMIA, Monarch Initiative). Gephebase contains more than 1700 entries. Each entry corresponds to an allelic difference at a given gene and its associated phenotypic change(s) between two species or two individuals of the same species, and is enriched with molecular details, taxonomic information, and bibliographic information. Users can easily browse entries and perform searches at various levels using boolean operators (e.g. transposable elements, snakes, carotenoid content, Doebley). Data is exportable in spreadsheet format. This database allows to perform meta-analyses to extract global trends about the living world and the research fields. Gephebase should also help breeders, conservationists and others to identify promising target genes for crop improvement, parasite/pest control, bioconservation and genetic diagnostic. It is freely available at www.gephebase.org.

Highlights

Mutations form the raw bulk of heritable variation upon which traits evolve
Identifying the DNA sequence modifications that drive phenotypic changes is a primary goal of modern genetics, and could greatly improve our understanding of the mechanisms behind biodiversity and adaptation
Compilations of genotype–phenotype relationships are available for a limited number of species in taxon-specific databases, for example OMIA for animals [4], OMIM for humans [5], TAIR for Arabidopsis [6], FlyBase for Drosophila [7], or the Monarch Initiative across the main laboratory animal model species [8,9]

Summary

Introduction

Mutations form the raw bulk of heritable variation upon which traits evolve. Identifying the DNA sequence modifications that drive phenotypic changes is a primary goal of modern genetics, and could greatly improve our understanding of the mechanisms behind biodiversity and adaptation. We developed Gephebase, a manually curated database that gathers published data about the genes and the mutations responsible for evolutionary changes in all Eukaryotes (mostly animals, yeasts and plants) into a single website. One entry corresponds to a single mutation, or a group of linked mutations within a single gene, that has been associated with a phenotypic trait.

Results

Conclusion