New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources

Abstract

Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease.

Keywords: Saccharomyces Genome Database; Saccharomyces cerevisiae; Alliance of Genome Resources; knowledgebase; reference genome.

Figure 1

SGD allele pages include (A) Overview with name, affected gene, type of allele, and a description of sequence change and/or domain mutated; phenotype annotations; (B) genetic interaction annotations; and (C) shared alleles network diagram depicting shared phenotypes and interactions with other alleles.

Figure 2

(A) SGD provides links between SGD gene pages and those for orthologous genes at the Alliance of Genome Resources. Hexagonal icons represent each organism (human, mouse, rat, zebrafish, fly, worm, and yeast) for which there is gene information at the Alliance. (B) Curated information from SGD is presented on yeast gene pages at the Alliance of Genome Resources. The various types of yeast data that can be found at the Alliance can be viewed using the menu on the left side of the gene page, and include orthologs, functional annotations using the GO, cellular pathways, phenotypes, disease associations, alleles, variants, sequence features, expression, and interactions. Data can be downloaded in bulk from https://www.alliancegenome.org/downloads.

Figure 3

SGD homology pages (A) include an overview of general information about the yeast gene, with links to homologous gene pages at the Alliance; (B) information about known homologs including species corresponding Gene ID, and name of the homolog; and (C) data about cross-species functional complementation between yeast and other species. Also included on the page, but not shown here, are Fungal Homologs, gene identifiers in other databases, and links to external resources.

Figure 4

SGD disease pages use the Disease Ontology to describe human diseases that are associated with yeast homologs, and include (A) disease annotation summary and individual annotations; and (B) shared annotation network that depicts shared disease annotations for other yeast genes and their human homologs.