henhaobio
Sign in

GeneticsGeneticsPeer-reviewed journal article

Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements

Stacia R. EngeliD, Suzi AleksanderiD, Robert S NashiD, Edith D. WongiD, Shuai WengiD, Stuart R. MiyasatoiD, Gavin J. SherlockiD, J. Michael CherryiD

PDFDOIPreprintData
In-depth full-text digest available · Jump to digest ↓

Abstract

Budding yeast (Saccharomyces cerevisiae) is the most extensively characterized eukaryotic model organism and has long been used to gain insight into the fundamentals of genetics, cellular biology, and the functions of specific genes and proteins. The Saccharomyces Genome Database (SGD) is a scientific resource that provides information about the genome and biology of S. cerevisiae. For more than 30 years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation for budding yeast along with search and analysis tools to explore these data. Here we describe recent updates at SGD, including the two most recent reference genome annotation updates, expanded biochemical pathways representation, changes to SGD search and data files, and other enhancements to the SGD website and user interface. These activities are part of our continuing effort to promote insights gained from yeast to enable the discovery of functional relationships between sequence and gene products in fungi and higher eukaryotes.

In-depth summary

Claude Opus 5.5 · xhigh effort · 8 Nov 2026 · from the full text of version 1 (20 Sept 2024) · CC BY 4.0

Saccharomyces Genome Database released two S288C annotation updates (R64.4.1, R64.5.1) adding ncRNAs, ORFs and uORFs, overhauled YeastPathways, and expanded search, GFF and web features.

Budding yeast results carry over to higher eukaryotes because many molecular mechanisms are conserved, so researchers rely on a current, curated reference annotation and on searchable functional and metabolic data. This update keeps the S288C annotation current, makes curated yeast metabolism usable for other species through BioPAX and Noctua, and moves SGD tools into the Alliance of Genome Resources.

Key results

  1. ShownReference annotation release R64.4.1 added noncoding RNAs and uORFs and downgraded weakly supported ORFs to Dubious. The S288C chromosome sequence was not changed.

    R64.4.1 (dated 2023-08-23): eight ncRNAs and three uORFs added; three ORFs moved from Uncharacterized to Dubious because they overlapped tRNAs, had multiple frameshifts and/or indels, and had minimal supporting evidence; genome sequence unchanged (Table 1). · Genome version R64.4.1; Tables

  2. ShownRelease R64.5.1 added new ORFs and uORFs, shifted the start of one ORF, and promoted one ORF from Dubious to Verified based on translation evidence. Chromosome sequences again stayed the same.

    R64.5.1 (dated 2024-05-29): six new ORFs and six new uORFs; one ORF given a shifted start; one ORF upgraded from Dubious to Verified after a stable translation product was detected; sequence unchanged (Table 2). · Genome version R64.5.1; Tables

  3. ShownYeastPathways got its first major content overhaul since 2012. Yeast-specific pathways were added, existing ones were revised, and the curated metabolism was exported to Noctua so it can be turned into GO annotations for yeast and orthologous genes.

    Database holds 220 conserved pathways; 62 updated with expert summaries; thirty-three yeast-specific pathways propagated from MetaCyc (SRI); 105 existing pathways corrected for enzyme classification, reaction connectivity and gene attribution; missing compound structures and reaction stoichiometry updated; BioPAX export loaded into Noctua. · BIOCHEMICAL PATHWAYS; Figure legends

  4. ShownSGD site search now covers more data types and fields, including datasets, strains, macromolecular complexes, alleles, RNA products and biochemical pathways.

    New Datasets category with over 3,700 yeast datasets searchable by reference, keyword, assay and lab; Strains subcategory under Reference; complexes searchable by alias, subunit, function, process, location; alleles by description, SGDID, type, gene, phenotype; RNAcentral IDs; Biochemical Pathways category with References and Loci facets plus autocomplete. · UPDATES TO SGD SEARCH; BIOCHEMICAL PATHWAYS

  5. ShownThe GFF3 file and supporting infrastructure were revised. Gene features now span the longest measured transcripts so the file works with JBrowse 2, YeastMine moved to AllianceMine, and Textpresso indexing became weekly.

    Since November 2020, transcript features use experimentally determined longest transcripts from galactose and dextrose media where available; in February 2024 gene entries were extended to cover them. YeastMine (InterMine-based, launched 2011) data now in AllianceMine; Textpresso refreshed weekly; ChEBI structures added to Chemical pages. · CHANGES TO SACCHAROMYCES CEREVISIAE GFF FILE; OTHER UPDATES TO THE WEB INTERFACE; FUTURE DIRECTIONS

Methods, data and reproducibility

SGD updates to the S288C reference annotation (new ncRNAs, ORFs and uORFs, plus status changes) and manual curation of YeastPathways, with pathways propagated from MetaCyc and exported in BioPAX to Noctua. The team also re-mapped site search, extended GFF3 gene coordinates for JBrowse 2, and moved YeastMine to AllianceMine.

  • S. cerevisiae S288C reference genome annotation, releases R64.4.1 (2023-08-23) and R64.5.1 (2024-05-29) · Saccharomyces cerevisiae (strain S288C)
  • YeastPathways manually curated metabolic pathways and their enzymes · Saccharomyces cerevisiae · n = 220 pathways
  • MetaCyc (SRI) pathways propagated into YeastPathways for yeast-specific biochemistry · n = Thirty-three new pathways
  • Experimentally determined longest transcripts in galactose and dextrose growth media, used for GFF transcript and gene features · Saccharomyces cerevisiae
  • Yeast datasets indexed in the new SGD search Datasets category · Saccharomyces cerevisiae · n = over 3,700 datasets
  • New yeast publications triaged weekly from PubMed and indexed in Textpresso for full-text search
  • ChEBI ontology chemical structures added to SGD Chemical pages
Methods & tools
Saccharomyces Genome Database (SGD), YeastPathways, MetaCyc, BioPAX, Noctua (GO Consortium), JBrowse 2, GFF3 (Generic Feature Format Version 3), InterMine / YeastMine, AllianceMine (Alliance of Genome Resources), Textpresso, ChEBI ontology, RNAcentral
Reproducibility gaps
No source-code repository for SGD software is cited, and the integrated BLAST tool based on SequenceServer had not been released when the paper was written.
Limitations (4)
  • Experimentally determined transcripts are available only for some genes and only for two growth media (galactose, dextrose). For genes without such data, GFF transcript features fall back to the ORF start and stop coordinates. · stated by the authors
  • Integration into the Alliance of Genome Resources is still in progress, and the integrated SequenceServer-based BLAST tool had not yet been released. · stated by the authors
  • The claimed gains in search relevance, efficiency and user satisfaction are not supported by usage statistics, query-level evaluation or user studies. · noted in this summary
  • Annotation changes are given only as feature counts. Which loci changed and what evidence supports the new ORFs, uORFs and ncRNAs is left to the tables, and the paper does not estimate how many uORFs or small ORFs remain unannotated. · noted in this summary

Read this if you use SGD reference annotation, GFF files, YeastMine or YeastPathways in yeast genomics or metabolism work and need to know what changed in R64.4.1, R64.5.1 and SGD tooling.

Citations
101
FWCI
13.70
Field percentile
top 1%

Reproducibility ledger

Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.

Sign in to file a reproducibility report.

Related papers

Similarity Map
SelectedSame fieldCross-field
THISEngel '21Dietrich '23Jia '26David '26Maclean '17Peris '22
83% semantic matchGenetics
Stacia R. Engel, Edith D. Wong, Robert S Nash+9 more·Genetics·Dec 13, 2021· 91 citations