New data and collaborations at theSaccharomycesGenome 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.

Fission stories: using PomBase to understand Schizosaccharomyces pombe biology

“…Human gene symbols ( Tweedie et al. 2021 ) or S. cerevisiae gene names, ORF names, or IDs ( Cherry et al 2012 ; Engel et al 2021 ) can also be used to find curated orthologs. Publication pages and ontology term pages can be retrieved using relevant IDs (PubMed or ontology IDs).…”

Harmonizing model organism data in the Alliance of Genome Resources

“…ACeDB for the Caenorhabditis elegans genome; Martinelli et al 1997 ). These include the Saccharomyces Genome Database (SGD, https://www.yeastgenome.org [accessed 2022 Jan 16]; Engel et al 2021 ), FlyBase ( https://flybase.org [accessed 2022 Jan 16]; Gramates et al 2022 ), WormBase ( https://wormbase.org [accessed 2022 Jan 16]; Davis et al 2022 ), Mouse Genome Informatics (MGI, http://www.informatics.jax.org/ [accessed 2022 Jan 16] ; Ringwald et al 2021 ), Rat Genome Database (RGD, https://rgd.mcw.edu/ [accessed 2022 Jan 16]; Smith et al 2020 , Kaldunski et al 2021 ), the Zebrafish Information Network (ZFIN, https://zfin.org [accessed 2022 Jan 16]; Bradford et al 2022 ), PomBase ( https://pombase.org [accessed 2022 Jan 16], Harris et al 2021 ), The Arabidopsis Information Resource (TAIR, https://arabidopsis.org [accessed 2022 Jan 16]; Berardini et al 2015 ), and Xenbase ( xenbase.org [accessed 2022 Jan 16], Fortriede et al 2020 ). These model organism databases (MODs), expanded in depth and scope as genomics and genome-scale experiments rose in prominence in the research community.…”

Heme Oxygenase-1 (HMX1) Loss of Function Increases the In-Host Fitness of the Saccharomyces ‘boulardii’ Probiotic Yeast in a Mouse Fungemia Model

“…Annotated VCF files were uploaded to FigShare ( (accessed on 29 March 2022)). Additionally, genetic and physical interactions involving HMX1 and its transcriptional regulators were extracted from the Saccharomyces Genome Database (accessed on 29 March 2022) [ 56 , 57 ] to allow evaluation of the data from the aspect of the heme oxygenase. Altogether, 4 genes with physical interactions and 88 with genetic interactions have been listed, along with 12 transcriptional regulators.…”

“…Fischer’s exact test was applied to test whether mutations affected HMX1 -interacting genes to a degree significantly different from non-interacting genes. GO term analysis to assess the potential enrichment of genes affected by medium- or high-effect mutations was performed on the Saccharomyces Genome Database (accessed on 5 March 2022) [ 56 , 57 ].…”