New & Noteworthy

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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