New & Noteworthy

Where to Order Yeast Strains: A Guide to Strain Resources

June 03, 2026

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 comprehensive 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, including:

• Addgene Plasmids – Plasmid repository
• DNASU Plasmids – Plasmid resource collection
• LibrarYeast – Yeast strain and plasmid libraries

Additional Major Yeast Strain Repositories

Beyond the resources linked on SGD Phenotype pages, here are other valuable repositories:

European Collections

Euroscarf (European Saccharomyces cerevisiae Archive for Functional Analysis) https://www.euroscarf.de/ One of the largest yeast strain collections, Euroscarf provides deletion mutants, overexpression strains, and other specialized collections for the research community.

National Collection of Yeast Cultures (NCYC) https://www.ncyc.co.uk/ Maintains over 4,000 yeast strains, including wild-type isolates and reference strains.

Industrial Yeasts Collection DBVPG https://dsa3.unipg.it/DBVPG/en/ Houses over 6,000 yeast strains with a focus on industrial and wild yeasts.

Common Access to Biological Resources and Information (CABRI) http://www.cabri.org/ Provides access to catalogs from multiple European culture collections.

North American Collections

ATCC (American Type Culture Collection) https://www.atcc.org/ A premier biological resource center offering authenticated yeast strains, including reference strains and mutant collections.

Specialized Collections and Commercial Sources

Schuldiner Lab Collections and Libraries https://mayaschuldiner.wixsite.com/schuldinerlab/lab-data Includes specialized strain collections and genomic libraries.

Creative Biogene Knockout Strains https://microbiosci.creative-biogene.com/saccharomyces-cerevisiae-s288c-knockout-strains-2644.html Offers S. cerevisiae S288C knockout strains.

Horizon Discovery Yeast Tools https://horizondiscovery.com/en/non-mammalian-research-tools/products/yeast-parental-strains Provides parental strains and yeast research tools.

Need Help?

If you’re having trouble locating a specific strain or accessing any of these resources, don’t hesitate to contact the SGD Helpdesk. We’re here to help connect you with the strains you need for your research.

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Categories: Tutorial

SGD Newsletter, May 2026

May 27, 2026

About this newsletter:
This is the May 2026 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.

Contents

• Join Us at Yeast Genetics Meeting 2026
• Introducing BLAST Search for SGD at the Alliance of Genome Resources
• Textpresso Literature Search: New Login System
• Naming Your Newly Characterized Yeast Gene: A Guide to SGD Gene Nomenclature
• Alliance of Genome Resources News
• microPublications – Latest Yeast Papers
• Upcoming Conferences & Courses
• The End of PomBase?
• In Memoriam: David Botstein

Join Us at Yeast Genetics Meeting 2026

Introducing BLAST Search for SGD at the Alliance of Genome Resources

What’s New

The Alliance BLAST service provides researchers with powerful sequence similarity search capabilities against SGD datasets, maintaining the functionality that the yeast research community has relied on for years while benefiting from the Alliance’s modern infrastructure and cross-species integration.

Key Features

• Comprehensive SGD datasets: Search against the complete S. cerevisiae genome, including coding sequences, proteins, and genomic DNA
• Familiar BLAST functionality: All standard BLAST algorithms (BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX) are supported
• Enhanced performance: Leveraging the Alliance’s updated infrastructure for faster search results
• Cross-species exploration: Seamlessly explore homologs across other Alliance member databases

Part of a Broader Migration

This BLAST service is part of our comprehensive strategy to transition SGD resources to the Alliance of Genome Resources. This migration ensures that:

• SGD data remains accessible and well-maintained for the research community
• Users benefit from integration with data from other model organisms
• Resources are consolidated on a sustainable, collaborative platform
• The yeast community gains access to enhanced comparative genomics tools

Visit the Alliance of Genome Resources to access the new services for SGD BLAST and Fungal BLAST. The datasets will be familiar to longtime SGD users.

We remain committed to supporting the yeast research community through this transition. Additional SGD tools and features will continue to migrate to the Alliance platform in the coming months. Stay tuned for updates, and as always, we welcome your feedback.

Textpresso Literature Search: New Login System

It’s particularly useful for finding specific mentions of genes, phenotypes, or experimental details that might not appear in article abstracts.

Naming Your Newly Characterized Yeast Gene: A Guide to SGD Gene Nomenclature

Alliance of Genome Resources News

Alliance of Genome Resources – Latest Releases 9.0.0 & 8.3.0

9.0.0 Release – May 13, 2026

The 9.0.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.

Updates and improvements have been made to the following pages:

• Non-gene genome features, e.g. enhancers, TF binding sites, etc.,  are now represented on their own respective “Gene” pages labeled as “GENOME FEATURE”. Examples include this enhancer page and this TF binding site page
• The gene page Alleles and Variants table now has fully functional filtering for Allele symbol and Variant name
• Allele page Genomic Variant Information and (high-throughput) Variant page Summary widgets now display the relevant genome assembly, thousand comma separators for genomic coordinates (for ease of reading), and symbol hyperlinks to JBrowse for the respective variant
• Note that rs IDs for variants are no longer used to construct URLs for high-throughput variants matching the rs IDs because a single rs ID can represent multiple individual variants for which we would like to render a Variant page. Instead, HGVS.g names are used as unique identifiers in URLs to point to distinct and individual variants in a more robust manner. An example of an rs ID use on the 8.3.0 release and prior is rs864303764 which enabled a single URL in those prior releases but did not adequately represent all three individual variants that the rs ID represents. These are now represented by URLs constructed based on the full HGVS.g name for each variant: NC_000085.7:g.3684464A>C, NC_000085.7:g.3684464A>G, and NC_000085.7:g.3684464A>T (example URL: https://www.alliancegenome.org/variant/NC_000085.7:g.3684464A>C) 
• Many high throughput variant insertions, deletions and indels had been mistakenly omitted from the Alliance variant data set, but have now been included for the 9.0.0 release
• This release makes available a large increase in the number of C. elegans alleles (~12K to ~1.9M) due to shifting data sources on our back end resources
• Gene page Summary widgets now display, where applicable, a gene systematic name (for fly, worm, and yeast genes) and UniProt Gene Centric Reference Proteome (GCRP) IDs, distinct from other UniProtKB IDs
• A number of significant backend changes have removed or modified existing Alliance public API endpoints. See release notes for examples.
  • All “Cache Search” endpoints have been removed. See release notes for examples.
  • All “Homology” endpoints have been removed (homology data can be extracted from the Orthology file on the Downloads page and endpoints for gene/orthologs and gene/paralogs). See release notes for examples.
  • Other select endpoints have been removed, replaced by the updated endpoints. See release notes for examples.
  • Modified endpoints are now compliant with our LinkML data model and deliver a different JSON format from previous releases. See release notes for examples.

8.3.0 Release – December 17, 2025

The 8.3.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.

Updates and improvements have been made to the following pages:

• The News page https://www.alliancegenome.org/news now includes a feed for the Alliance Mastodon account.

• The Alliance BLAST Service page https://www.alliancegenome.org/blastservice has been updated to include fly, worm, yeast, fungal, and rat BLAST services. This BLAST service allows researchers to search genomic sequences using the Basic Local Alignment Search Tool (BLAST). By entering a sequence or query, users can find regions of similarity to various genomes within the Alliance. This service supports separate environments for each of the Model Organism Databases (MODs) as well as a unified environment for the Alliance. Results provide detailed alignments and annotations to aid in your research.
• Gene page transgenic alleles tables have been updated with improved filter and sort options, and now include alleles where the focus gene plays a regulatory role in transgenic constructs.
• Gene page expression data now features enhanced sorting capabilities and clearer formatting in downloadable files.

microPublications – Latest Yeast Papers

​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 microPubublications when you have a result that doesn’t necessarily fit into a larger story, but will be of value to others. Latest yeast microPublications:

• Wang TK, et al. (2026) A cross-species rescue by mating method to interrogate gene essentiality across the Saccharomyces genus. MicroPubl Biol. 2026 Mar 27;2026:10.17912/micropub.biology.002022. doi: 10.17912/micropub.biology.002022. eCollection 2026.
• Brown K, Singuluri H, Perkins F, Kuchin S (2026) The N-terminal α helix domain of the mitochondrial VDAC protein Por2 is dispensable for promoting the nuclear localization of yeast AMPK. MicroPubl Biol. 2026 Feb 23:2026:10.17912/micropub.biology.001040. doi: 10.17912/micropub.biology.001040. eCollection 2026.
• Ackermann LM, Ro A, Dunn B, Moore R, Doss G, Armstrong JO, Dunham MJ (2026) Using Experimental Evolution to Correct Mother-Daughter Separation Defects in Brewing Yeast. MicroPubl Biol. 2026 Feb 13:2026:10.17912/micropub.biology.001962. doi: 10.17912/micropub.biology.001962. eCollection 2026.
• Klepin S, Michalik B, Pillus L, Chik JK (2025) Mutation of a conserved anthranilate phosphoribosyltransferase active site residue supports tryptophan biosynthesis in vivo. MicroPubl Biol. 2025 Dec 15:2025:10.17912/micropub.biology.001925. doi: 10.17912/micropub.biology.001925. eCollection 2025.
• Beckwith SL (2025) Co-expression of a retrotransposon and re-targeted restriction factor impairs yeast growth. MicroPubl Biol. 2025 Nov 3:2025:10.17912/micropub.biology.001905. doi: 10.17912/micropub.biology.001905. eCollection 2025.

Upcoming Conferences & Courses

• Yeast Genetics Meeting 2026
  • June 13 to June 17, 2026 –
  • Asilomar Conference Grounds, Pacific Grove, CA
• Chromosome Biology and Cell States in Yeasts
  • July 27 to July 29, 2026 –
  • Niagara Falls Convention Center, Niagara Falls, NY
• 41st SMYTE Small Meeting on Yeast Transport and Energetics
  • September 12 to September 16, 2026 –
  • Chaves, Portugal
• 39th International Specialized Symposium on Yeasts (ISSY39)
  • November 08 to November 12, 2026 –
  • Seoul, South Korea

The End of PomBase?

This decision places PomBase on a path to closure. Without alternative support, which at present seems unlikely, Pombase will lose not only the database but also the specialist expertise required to curate, maintain, and develop it. All three staff are funded entirely through grants; when funding stops, the resource and the knowledge behind it disappear together.

PomBase, like SGD, is a core piece of scientific infrastructure. It underpins research far beyond the yeast community, enabling discovery, reproducibility, and data integration across the life sciences. Losing it would not be a local setback; it would be a permanent loss to the global research ecosystem.

This is not just about PomBase. Essential bioinformatics resources are at risk. Other model organism databases, like SGD and Flybase, are under the same funding squeeze. FlyBase now requires support by direct fees from the community to sustain its curation. The wider scientific community must choose to sustain the shared infrastructure that drives modern biology and innovation. The contraction of funding has exposed a systemic vulnerability in how we fund biological data resources. We urge funders, institutions, and the community to recognize what is at stake. Once lost, resources like PomBase, Flybase, and SGD cannot simply be rebuilt.

In Memoriam: David Botstein

David’s scientific impact is vast and enduring. He co-authored the landmark 1980 paper introducing the use of restriction fragment length polymorphisms (RFLPs) for human genetic mapping, a conceptual breakthrough that opened the door to finding disease genes well before whole-genome sequencing was possible. He later helped usher in the era of genome-wide expression analysis, demonstrating how systematic measurement and clustering of gene expression could illuminate cellular pathways, regulatory programs, and physiological states. Across decades, his work, leadership, and mentorship helped define the fields of genetics and genomics.

Yeast, and the global community that studies it, benefited enormously from David’s clarity of thought and sense of purpose. He championed model organisms as engines of insight, insisting that fundamental principles uncovered in yeast could illuminate biology more broadly. From the beginning, he advocated for standards, reproducibility, and open data, principles that remain at the heart of SGD. Many of the practices we still rely on, including careful literature-based curation, genotype-to-phenotype integration, and community engagement, grew directly from his vision.

David was also a gifted mentor and collaborator. He trained and inspired generations of scientists, curators, engineers, and students, encouraging bold ideas and rigorous tests of those ideas. Those who worked with him remember his incisive questions, his generosity with time and credit, and his unwavering commitment to getting the science right. His influence extends through the many people he mentored and the communities and institutes he helped build at MIT, Stanford, Princeton, and beyond.

To the SGD team, David’s legacy is personal. We have been honored to steward a resource he helped bring into being, and we remain committed to the principles he championed: accuracy, openness, and service to the community.

We extend our deepest condolences to David’s family, friends, colleagues, and the many people around the world who learned from and were inspired by him.

Note: If you wish to receive this newsletter via email, please contact the SGD Help Desk at sgd-helpdesk@lists.stanford.edu.

Categories: Newsletter

Tags: Newsletter

How to Find UTR Lengths for Yeast Genes

May 21, 2026

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:

• 5′ UTRs: http://sgd-archive.yeastgenome.org/sequence/S288C_reference/SGD_all_ORFs_5prime_UTRs.fsa.zip
• 3′ UTRs: http://sgd-archive.yeastgenome.org/sequence/S288C_reference/SGD_all_ORFs_3prime_UTRs.fsa.zip

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.

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Have questions about yeast genomics data? Contact the SGD Helpdesk! We’re here to help you find the information you need for your research.

Categories: Tutorial

Adding a New Gene to the Reference Genome Annotation

April 23, 2026

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.

Questions?

The SGD team is here to help! If you have questions about genome sequence annotations, please don’t hesitate to contact us at sgd-helpdesk@lists.stanford.edu.

Categories: Tutorial

Naming Your Newly Characterized Yeast Gene: A Guide to SGD Gene Nomenclature

April 03, 2026

Have you discovered the function of a previously uncharacterized Saccharomyces cerevisiae gene? Here’s everything you need to know about giving it an official standard name.

Understanding Yeast Gene Nomenclature

SGD maintains the S. cerevisiae nomenclature according to guidelines established by the yeast research community. These conventions ensure consistency and clarity across the field, making it easier for researchers worldwide to communicate about genes and their functions.

The Naming Rules

Valid standard names for S. cerevisiae ORFs follow a simple but important format:

• Three letters followed by a number (for example, COX2 or CDC28)
• Must be unique, not previously used to describe another yeast gene
• Should ideally reflect function when possible

This naming convention has served the yeast community well for decades, creating an intuitive system where gene names often provide immediate clues about biological roles.

How to Reserve Your Gene Name

If you’re preparing to publish work on a gene that currently has only a systematic name (like YAL037W), reserve a standard name through SGD before publication. Here’s how:

The Reservation Process

1. Submit early: Reserve your gene name before you publish. A gene name reservation is valid for twelve months, which is typically enough time to write, submit, and publish your manuscript.
2. Access the reservation form: Visit https://www.yeastgenome.org/reserved_name/new, or navigate from any SGD page using the purple toolbar at the top: Community > Nomenclature > Submit a Gene Registration.
3. Publication makes it official: Your reserved gene name will become the standard gene name upon publication.

Best Practices for Publication

When you’re ready to publish, we recommend:

✓ Double-check the literature to ensure your chosen name is still unique
✓ Include both the ORF name and gene name in your abstract – this helps SGD and other databases find and curate your paper efficiently
✓ Verify your reservation is still active if your publication timeline will extend beyond the initial twelve-month period

Need More Information?

The complete gene naming process is described in detail in our Gene Naming Guidelines.

Questions?

The SGD team is here to help! If you have questions about the gene name reservation process or nomenclature guidelines, please don’t hesitate to contact us at sgd-helpdesk@lists.stanford.edu.

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Contributing to yeast nomenclature is an important part of advancing our collective understanding of this remarkable model organism. Thank you for following these guidelines and helping maintain the clarity and consistency of yeast gene names!

Categories: Tutorial

In Memoriam: David Botstein

March 02, 2026

We are deeply saddened to share the news of the passing of David Botstein, a towering figure in modern genetics and a foundational force behind the Saccharomyces Genome Database (SGD). SGD began in the early 1990s in David’s lab at Stanford University, and his vision for a rigorously curated, community-centered resource set the course for what SGD is today. His belief that carefully organized, interoperable data would accelerate discovery has guided our work from the start and continues to shape our mission.

David’s scientific impact is vast and enduring. He co-authored the landmark 1980 paper introducing the use of restriction fragment length polymorphisms (RFLPs) for human genetic mapping, a conceptual breakthrough that opened the door to finding disease genes well before whole-genome sequencing was possible. He later helped usher in the era of genome-wide expression analysis, demonstrating how systematic measurement and clustering of gene expression could illuminate cellular pathways, regulatory programs, and physiological states. Across decades, his work, leadership, and mentorship helped define the fields of genetics and genomics.

Yeast, and the global community that studies it, benefited enormously from David’s clarity of thought and sense of purpose. He championed model organisms as engines of insight, insisting that fundamental principles uncovered in yeast could illuminate biology more broadly. From the beginning, he advocated for standards, reproducibility, and open data, principles that remain at the heart of SGD. Many of the practices we still rely on, including careful literature-based curation, genotype-to-phenotype integration, and community engagement, grew directly from his vision.

David was also a gifted mentor and collaborator. He trained and inspired generations of scientists, curators, engineers, and students, encouraging bold ideas and rigorous tests of those ideas. Those who worked with him remember his incisive questions, his generosity with time and credit, and his unwavering commitment to getting the science right. His influence extends through the many people he mentored and the communities and institutes he helped build at MIT, Stanford, Princeton, and beyond.

To the SGD team, David’s legacy is personal. We are honored to steward a resource he helped bring into being, and we remain committed to the principles he championed: accuracy, openness, and service to the community. As we continue to evolve SGD in a multi-omic, data-rich era, we do so with gratitude for the foundation he laid and the example he set.

We extend our deepest condolences to David’s family, friends, colleagues, and the many people around the world who learned from and were inspired by him.

Categories: News and Views

Introducing BLAST Search for SGD at the Alliance of Genome Resources

February 17, 2026

We’re excited to announce the launch of a new BLAST service for Saccharomyces Genome Database (SGD) data, now available at the Alliance of Genome Resources. This release marks another significant milestone in our ongoing effort to migrate SGD services and data to the Alliance platform, ensuring continued access to essential yeast genomics tools within an integrated, multi-organism framework.

What’s New

The Alliance BLAST service provides researchers with powerful sequence similarity search capabilities against SGD datasets, maintaining the functionality that the yeast research community has relied on for years while benefiting from the Alliance’s modern infrastructure and cross-species integration.

Key Features

• Comprehensive SGD datasets: Search against the complete S. cerevisiae genome, including coding sequences, proteins, and genomic DNA, or search against genomes from dozens of other strains
• Familiar BLAST functionality: All standard BLAST algorithms (BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX) are supported
• Enhanced performance: Leveraging the Alliance’s updated infrastructure for faster search results
• Cross-species exploration: Seamlessly explore homologs across other Alliance member databases

Part of a Broader Migration

This BLAST service is part of our comprehensive strategy to transition SGD resources to the Alliance of Genome Resources. This migration ensures that:

• SGD data remains accessible and well-maintained for the research community
• Users benefit from integration with data from other model organisms
• Resources are consolidated on a sustainable, collaborative platform
• The yeast community gains access to enhanced comparative genomics tools

Getting Started

Visit the Alliance of Genome Resources to access the new service for SGD BLAST, including Fungal BLAST. The datasets will be familiar to longtime SGD users.

Looking Ahead

We remain committed to supporting the yeast research community through this transition. Additional SGD tools and features will continue to migrate to the Alliance platform in the coming months. Stay tuned for updates, and as always, we welcome your feedback.

Categories: Announcements

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