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SGD Newsletter, August 2026

August 20, 2026

About this newsletter:
This is the August 2026 issue of the SGD newsletter. This issue features a celebration of the 30th anniversary of the first eukaryotic genome sequence, a suite of powerful new SGD features including Pathway Pages and Functional Networks, and practical guides to help you get the most out of your yeast research.

Contents

Celebrating 30 Years Since the First Eukaryotic Genome

This year marks the 30th anniversary of a landmark achievement in biology: the publication of the complete Saccharomyces cerevisiae genome sequence in 1996 – the first eukaryotic genome ever sequenced.

Since before the genome was even complete, SGD has served as the authoritative resource for yeast genomics. Over three decades, we’ve evolved from a simple sequence repository to a comprehensive biological knowledge hub, providing expert curation and multi-dimensional annotations that support researchers worldwide.

A special meeting, Life with 6000 Genes, takes place August 31 – September 1, 2026 to commemorate this milestone and the remarkable era of discovery it enabled.

To mark this anniversary, SGD team members have authored a retrospective chronicling our 32-year history, from the founding vision through today’s collaborative database ecosystem. The article will appear in a special issue of FEMS Yeast Research.

Thank you to the yeast research community for three decades of collaboration, contributions, and discoveries!

New Pathway Pages: Comprehensive Views of Yeast Biochemical Pathways

SGD now has Pathway Pages – dedicated pages for each of the 220 manually curated biochemical pathways in yeast.

Pathway pages offer a complete view of specific biochemical pathways in Saccharomyces cerevisiae. Each page integrates information from multiple sources to help you understand what the pathway does, which genes are involved, how gene products interact, and which chemicals are involved.

Interactive Pathway Diagrams

Each pathway page features a pathway diagram showing the chemical reactions and metabolic flow. The diagram displays:

  • Chemical compounds involved (substrates and products)
  • Enzymes catalyzing each reaction
  • Reaction directionality and relationships

A “View interactive diagram at YeastPathways” button takes you to the full interactive version where you can explore the pathway in greater detail.

Pathway Summary

Expert-curated descriptive text explains:

  • What the pathway does and why it’s important
  • Biological context and cellular roles
  • Connections to other metabolic processes
  • Key regulatory mechanisms

For example, the glyoxylate cycle page explains how this essential pathway allows yeast to grow on two-carbon compounds and its role in providing precursors for biosynthesis.

Genes Involved

A comprehensive table of genes participating in the pathway includes:

  • Gene names (standard and systematic)
  • EC numbers for enzymatic activities
  • Functional descriptions
  • Direct links to gene pages for detailed information

This makes it easy to see all the players in a pathway at a glance and access detailed information on any gene of interest.

Functional Networks

Pathway pages now include the same Functional Networks features available on gene pages:

Shared Annotations Network: Visualizes how genes in the pathway share phenotype and GO annotations, helping you identify:

  • Functional relationships between pathway genes
  • Connections to genes in related pathways
  • Potential regulatory relationships

You can filter the network by the number of shared pathway genes to focus on the most relevant connections.

GO-CAMs: When available, Gene Ontology Causal Activity Model pathway models are displayed, showing:

  • Causal relationships between molecular activities
  • How gene products work together mechanistically
  • Regulatory interactions and dependencies

If multiple GO-CAM models involve genes from the pathway, you can switch between them using a dropdown menu.

GO Enrichment Analysis

The GO Enrichment section shows which biological processes are statistically overrepresented among pathway genes. This helps you:

  • Understand the broader biological context
  • See connections to related processes
  • Identify key functional themes

Each enriched term links to the genes involved and shows the statistical significance (p-value).

Browse All Pathways

Explore all 220 curated pathways:

Explore the Redesigned SGD Search Landing Page

SGD’s search landing page has been redesigned to make it easier to find the yeast biological information you need.

Enhanced Search Experience The new landing page features an improved search box with smart autocomplete functionality that suggests genes, chemicals, pathways, and other entities as you type. This makes searching faster and helps you discover relevant results even if you’re not sure of the exact name.

Quick Category Browsing Need to browse rather than search? The new page includes quick access buttons for popular categories including genes, complexes, pathways, and chemicals. Click any category to start exploring without typing a single character.

Advanced Filtering Refine your search results by category or other criteria to quickly zero in on exactly what you’re looking for. The redesigned interface provides clearer visual organization with distinct sections for different data types.

Stay Current with SGD The right side of the page now highlights SGD’s latest activity:

  • New Literature Added shows the most recently curated publications
  • Recent Annotations displays the latest curated data, including new phenotypes, alleles, and GO annotations

This makes it easy to stay up-to-date with the newest information added to SGD.

There are two easy ways to reach the new search landing page:

  1. Click the red “Explore SGD” button on the SGD homepage
  2. Press return/enter in the search box without typing anything (empty search)

Or go directly to: https://www.yeastgenome.org/search

Happy exploring!

New Filtering Options on the Yeast Papers Page

The New Yeast Papers page at SGD (yeastgenome.org/reference/recent) is your rolling monthly snapshot of publications newly added to the database, now with filtering options to help you find the papers most relevant to your research.

The page has always been a great way to stay current with Saccharomyces cerevisiae research, listing newly-added publications over the last 30 days along with the genes, alleles, complexes, and pathways associated with each paper. It’s updated daily, and now you can filter it by:

  • Author: find papers by a specific researcher
  • Journal: browse what’s new in your favorite publications
  • Year: narrow the list by publication year
  • Associated genes: zero in on papers linked to your gene of interest
  • Associated alleles: filter by specific alleles
  • Associated complexes: find papers connected to a complex you’re studying
  • Associated pathways: focus on your pathway of interest

Each filter shows the most frequently occurring values along with reference counts, giving you an at-a-glance view of what’s trending in this month’s yeast literature. Combine multiple filters to get as specific as you need, and use Clear all filters to reset. And as always, you can download the full reference list in .nbib format for your reference manager.

Access the New Yeast Papers page anytime via the Literature menu in the purple SGD navigation bar, or from SGD’s new Search landing page (bookmark this!) or go directly to yeastgenome.org/reference/recent. Happy reading!

Overhauled Complex Pages: Enhanced Data Access and Improved User Experience

SGD’s macromolecular complex pages have been overhauled to make complex information more accessible, comprehensive, and easier to navigate.

Why Protein Complexes Matter

Protein complexes are fundamental functional units in cells that operate as groups of proteins that work together to carry out specific biological processes. Since 2019, SGD has provided detailed information about yeast protein complexes, including subunit composition, functions, interactions, and references.

All Gene Ontology Information on One Page

One of the most significant improvements is the reorganization of Gene Ontology (GO) annotations. Previously, GO information was tucked away on a separate tab, requiring you to navigate away from the main view. Now, all GO annotations are prominently displayed right on the Summary page.

What you can see at a glance:

  • Molecular Function: What the complex does
  • Biological Process: What pathways or processes it participates in
  • Cellular Component: Where in the cell it’s located

All three are now visible directly on the Summary page.

GO-CAM Pathway Models for Complexes

We’ve also integrated GO-CAM (Gene Ontology Causal Activity Models) pathway models directly into complex pages. When available, these models appear below the GO annotations, showing how entire protein complexes fit into larger biological pathways and regulatory networks.

Enhanced Composition Section

Stoichiometry Data: For complexes where the subunit ratios have been experimentally determined, you’ll now see the exact stoichiometry, providing quantitative information about complex architecture.

Structural Information:

  • Expert-curated notes about complex assembly and structural features
  • Direct links to Protein Data Bank (PDB) entries for complexes with experimentally determined 3D structures
  • Protein-protein binding regions and interaction interfaces (when characterized)

Organized Display: Subunits are now grouped by their roles or relationships within the complex, making it easier to understand how the complex is organized.

Easy Navigation: Each subunit links directly to its SGD gene page, so you can access detailed information on individual components.

Shared Biology Networks

Complex pages now include a Shared Biology section that shows GO annotations shared with other complexes, subunits shared between complexes, and ranked lists that prioritize the most functionally related complexes.

Improved User Experience Throughout

  • Clearer section headers make information easy to find
  • Better spacing and organization improve readability
  • Consistent styling with other SGD page types provides a unified experience
  • Logical information hierarchy puts the most commonly accessed data front and center

Functional Networks: Visualizing Gene Relationships at SGD

New Functional Networks sections are now available on gene and complex pages. This addition helps researchers understand how genes and proteins work together in biological systems.

Shared Annotations Networks

Ever wondered which other genes might have similar functions to your gene of interest? The Shared Annotations network visualizes genes that share similar Gene Ontology (GO) annotations with your query gene. These networks are generated based on overlapping GO terms across Molecular Function, Biological Process, and Cellular Component.

Why is this useful?

  • Identify potential interaction partners
  • Find paralogs with related functions
  • Discover genes that may participate in similar biological processes
  • Generate hypotheses for experimental design

Most genes in the S. cerevisiae genome have sufficient GO annotations to generate these networks, providing broad coverage across the yeast proteome.

GO-CAM Pathway Models

GO-CAMs (Gene Ontology Causal Activity Models) represent an exciting advancement in pathway representation. Unlike traditional GO annotations that link individual genes to single terms, GO-CAMs show how multiple gene products work together in integrated pathway models with causal relationships showing how one molecular activity leads to another.

What makes GO-CAMs special?

  • Causal relationships: See how one molecular activity leads to another, including activation, inhibition, and regulatory interactions
  • Integrated view: Combines Molecular Function, Biological Process, and Cellular Component information in one unified model
  • Evidence-based: All models are manually curated by expert biologists and supported by published experimental data

Currently, 470 yeast genes are associated with GO-CAM models, and this number continues to grow as additional pathways are curated.

When multiple GO-CAM models are available for a gene, you can easily switch between them using a pull-down menu. Each model includes a “View GO-CAM at Gene Ontology” link that opens the interactive pathway in AmiGO, where you can explore detailed evidence codes, supporting references, and connections to other pathways.

Functional Networks on Complex Pages

We’ve also added a Shared Biology section to macromolecular complex pages. This section shows:

  • GO annotations shared with other complexes
  • Subunits shared between complexes
  • A ranked list summarizing these relationships

This helps researchers understand how protein complexes relate to each other and identify functionally similar complexes.

How to Access

Simply navigate to any gene page at SGD and scroll to the Functional Networks section (located beneath Gene Ontology). For complex pages, look for the Shared Biology section.

Part of a Bigger Picture

The GO-CAM display on SGD gene pages replicates the implementation from the Alliance of Genome Resources, providing a consistent user experience across model organism databases. This integration reflects our commitment to making yeast data accessible and interoperable with other genomic resources.

Redesigned Chemical Pages: Comprehensive Small Molecule Information in One Place

SGD’s chemical pages have been redesigned to provide comprehensive information about small molecules relevant to yeast biology such as metabolites, drugs, and experimental compounds, all in a more accessible, more user-friendly format.

Small molecules play crucial roles in yeast biology, from essential metabolites that keep cells functioning to experimental compounds that reveal how cellular processes work. SGD chemical pages bring together curated information about how these chemicals affect yeast, connecting chemical entities to genes, phenotypes, and biological pathways.

Chemical Structures Front and Center

The redesigned pages now display interactive 2D chemical structures prominently at the top of each page. These structures clearly show molecular connectivity and functional groups, providing immediate visual recognition of the compound.

All Information on One Page

No need to navigate between multiple tabs! Everything you need to know about a chemical is now presented on a single, unified page:

Comprehensive Identifiers and Database Links:

This integration makes it easy to explore the chemical across multiple resources and access broader chemical and metabolic information.

Curated Experimental Data

Each chemical page now includes rich experimental data curated from the yeast literature:

Phenotype Annotations
See the effects of the chemical on yeast:

  • Growth effects
  • Metabolic changes
  • Other cellular processes

This section includes annotation statistics, top genes and phenotypes involving each chemical. Every phenotype annotation is linked to supporting experimental evidence and literature references, so you can trace findings back to the original research.

Gene Ontology Annotations and Enrichment

The GO Annotations section shows how the chemical is annotated within the Gene Ontology framework, connecting it to specific biological processes, molecular functions, and cellular components.

For metabolites, you’ll also find links to relevant metabolic pathways in YeastPathways throughout the GO annotation tables, connecting chemical entities to their biological context in small molecule metabolism.

The GO Enrichment section shows which biological processes and molecular functions are significantly associated with genes affected by the chemical, helping you:

  • Understand the broader biological context of chemical-gene interactions
  • Identify patterns in how chemicals influence cellular systems
  • Generate hypotheses about mechanism of action

Shared Chemicals Network

The Shared Chemicals section displays other chemical entities that share similar properties, annotations, or biological roles. This makes it easy to:

  • Explore chemical families
  • Find compounds with similar effects
  • Identify potential alternative compounds for experiments

Complete Literature Coverage

The References section compiles all publications from which data about the chemical has been curated. This provides direct access to the primary literature and shows you the full scope of research on each compound.

How to: Add a New Gene to the Reference Genome Annotation

SGD maintains the most up-to-date version of the complete genomic sequence of S. cerevisiae strain S288C. If your lab has characterized a gene or genomic feature that isn’t yet annotated, getting it added is a meaningful contribution. Here’s what SGD needs from you to do that:

Publicly Available Data

SGD only adds features based on published data. All coordinates, strand information, and sequence data must already be explicitly reported in a peer-reviewed publication. Depositing the sequence, including the genome sequence version used, in a public repository such as GenBank is also required.

What Should be Included in the Publication:

  • Explicit chromosomal coordinates, including genome sequence version used — stated in the text or a supplemental table, not only inferred from a figure or visualization
  • Strand orientation — sense (+) or antisense (–)
  • Strain background — SGD is built on S288C; note if your data maps to a different strain such as SK1 or W303
  • Feature type — protein-coding gene, ncRNA, pseudogene, regulatory region, etc.
  • GenBank Accession — Accession number from GenBank to identify the feature

When to Reach Out

Genome annotation updates at SGD are released periodically rather than continuously. When a new feature is identified, it is added to the list of new features that will be reviewed for incorporation into the next update. There are three good moments to contact us at sgd-helpdesk@lists.stanford.edu:

Before publication — if your paper is in preparation or under review, reaching out early lets curators know to watch for it. They can review the manuscript details and be ready to act as soon as it is accepted and assigned a PMID.

At or after publication — once your paper is published and indexed in PubMed, contact us with the PMID and point curators to where the relevant data appear in the paper.

If your paper is already in SGD but the feature is missing — SGD has curated thousands of papers and may have captured some findings from a publication while missing others. If you notice that a gene from your own work hasn’t been annotated, let us know and we will revisit the paper.

How to: Find UTR Lengths for Yeast Genes

Have you ever wondered where you can find information about the 5′ and 3′ UTRs (untranslated regions) for a list of yeast genes? If you’re working with Saccharomyces cerevisiae and need UTR information, we have several solutions depending on your needs.

Option 1: Bulk Download Files for Large Datasets

If you’re analyzing multiple genes or need comprehensive UTR data, downloading our complete datasets is the most efficient approach.

Access the SGD Downloads site: http://sgd-archive.yeastgenome.org/sequence/S288C_reference/

Download these two files:

These files contain FASTA-formatted sequences for all annotated ORF UTRs in the yeast genome. Once you download and extract the files, you can easily parse the sequences to determine lengths for your genes of interest. README files with additional details are located in the same folder.

Option 2: Query Individual Genes or Gene Lists with AllianceMine

For looking up UTR data on individual genes or specific gene lists, use the Gene -> UTRs template in AllianceMine:

https://www.alliancegenome.org/bluegenes/alliancemine/templates/Gene_UTRs

This tool allows you to input your genes of interest and retrieve UTR information in a structured, easy-to-use format.

Option 3: Browse UTRs Visually with JBrowse

If you prefer to explore UTR features in their genomic context, check out the UTR tracks in SGD’s JBrowse genome browser: https://jbrowse.yeastgenome.org

The visual browser lets you see UTRs alongside other genomic features, making it ideal for examining individual loci or exploring chromosomal regions.

Resource Guide: Where to Order Yeast Strains

One of the most frequent questions we receive at the SGD Helpdesk is: “Where can I order yeast strains for my research?” We’ve compiled a guide to help you locate the strains you need, whether you’re looking for deletion mutants, specific genetic backgrounds, or specialized collections.

Finding Strains Through SGD

SGD makes it easy to locate available strains directly from gene pages. Here’s how:

  1. Start at the Locus Summary page for your gene of interest (example: https://www.yeastgenome.org/locus/S000005000)
  2. Click on the “Phenotype” tab to navigate to the Phenotype Details page (example: https://www.yeastgenome.org/locus/S000005000/phenotype)
  3. Scroll to the “Resources” section at the bottom of the page

The Resources section includes direct links to several strain resources:

European Collections

  • Euroscarf (European Saccharomyces cerevisiae Archive for Functional Analysis) — One of the largest yeast strain collections, providing deletion mutants, overexpression strains, and other specialized collections.
  • National Collection of Yeast Cultures (NCYC) — Maintains over 4,000 yeast strains, including wild-type isolates and reference strains.
  • Industrial Yeasts Collection DBVPG — Houses over 6,000 yeast strains with a focus on industrial and wild yeasts.
  • CABRI (Common Access to Biological Resources and Information) — Provides access to catalogs from multiple European culture collections.

North American Collections

  • ATCC (American Type Culture Collection) — A premier biological resource center offering authenticated yeast strains, including reference strains and mutant collections.

Specialized Collections and Commercial Sources

Alliance of Genome Resources News

Alliance of Genome Resources – Advance Release Notes: 9.1.0

alliance logo.png

The following release notes are being published in advance of an upcoming release of the Alliance of Genome Resources website and dataset, expected August/September 2026, to give ample warning to Alliance end users and developers that data and/or APIs are changing so that they can update their data pipelines accordingly. Until the release goes live, some links and references may not have yet taken effect.

The 9.1.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.

As of release 9.1.0, there are new Genes and Phenotypes download files on the Alliance Downloads page. Prior releases included Gene Descriptions downloadable files; these files have been removed and replaced by the new Genes download files that contain the respective gene descriptions. All downloadable JSON file formats and some TSV file formats have changed.

Several API endpoints have changed their response payload format to include new, richer data and JSON files formatted according to the Alliance LinkML Data Model, including all endpoints that return download files available on the Alliance Downloads page. These include the following endpoints:

Several TSV files have changed format, including:

  • Variant-Allele TSV download will no longer have the “Variant Id” column (column 6) in favor of the “Variant Symbol” column providing the HGVS name of the variant
  • Disease association TSV download will have new columns — see the full release notes for the complete column specification
  • VCF files now have an additional header line (##reference) to declare the genome assembly version used across the whole file

Note that stable URLs for Alliance download files have changed in many instances and likely need to be updated in downstream consuming applications. For example, the all species disease JSON download stable URL has changed from: https://fms.alliancegenome.org/download/DISEASE-ALLIANCE-JSON_COMBINED.json.gz

to: https://www.alliancegenome.org/download/DISEASE-ALLIANCE_JSON_COMBINED.json.gz

Additional API changes affect disease annotation endpoints and phenotype annotation endpoints. See the full release notes for complete details.

microPublications – Latest Yeast Papers

MicroPub.png

microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative.

Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral. Consider microPublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others. Latest yeast microPublications:

Upcoming Conferences & Courses

Note: The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

Categories: Uncategorized

Tags: Newsletter , Saccharomyces cerevisiae , yeast