SGD Help: Reference Genome Sequence

View a quick video tutorial about different ways to access the yeast Reference Genome sequence and its annotation in SGD.

The annotation of the Saccharomyces cerevisiae strain S288C Reference Genome Sequence in SGD is described in different ways on different pages.

• The original genome sequence released in 1996 is described in the Systematic Sequencing Table.

• Current annotation details for each chromosome can be accessed via Chromosome pages.

• Complete summaries of sequence and/or annotation updates made for each chromosome, since the initial genome release on 1996-07-31, are available via Chromosome History pages.

• Access to GenBank and RefSeq files for the 16 nuclear chromosomes and mitochondria of the S288C Reference Genome is available from SGD's S288C strain overview.

• The release dates of all S. cerevisiae S288C genome releases are listed in the dates_of_genome_releases.tab file on SGD's Downloads site.

• Compressed data files relevant to the current and archived genome releases of the S. cerevisiae strain S288C reference genome sequence and annotation can also be accessed via SGD's Downloads site.

• The latest GFF is available from SGD's Downloads site.

Release Notes

Saccharomyces cerevisiae strain S288C Genome Annotation Release R64.5.1 (May 2024). 

• The S. cerevisiae strain S288C reference genome annotation was updated. The new genome annotation is release R64.5.1, dated 2024-05-29.Note that the underlying genome sequence itself was not altered. The chromosome sequences remain stable and unchanged.

• This annotation update included:

  • new ORFs: YDL204W-A, YFR035W-A, YGR016C-A, YMR106W-A, YNL040C-A, YNL155C-A

  • new uORFs for existing ORFs: ATG12/YBR217W, ATG19/YOL082W, ATG5/YPL149W, ATG13/YPR185W

  • move start downstream: EFM4/YIL064W

  • ORF upgraded from Dubious to Verified: YIL059C

Saccharomyces cerevisiae strain S288C Genome Annotation Release R64.4.1 (September 2023)

• The S. cerevisiae strain S288C reference genome annotation was updated. The new genome annotation is release R64.4.1, dated 2023-08-23. Note that the underlying genome sequence itself was not altered in any way.

• This annotation update included:

  • new uORFs for 3 ORFs: FPS1/YLL043W, ACC1/YNR016C, HOL1/YNR055C

  • 8 new ncRNAs: SUT035/YNCC0015W, SUT053/YNCD0033W, SUT468/YNCD0034C, SUT532/YNCG0047C, SUT125/YNCG0048W, SUT126/YNCG0049W, SUT390/YNCP0025W, SUT418/YNCP0026W

  • 3 ORFs demoted from ‘Uncharacterized’ to ‘Dubious’ based on request from NCBI because they overlap tRNAs: YDR278C, YOL013W-A, YPR108W-A

Saccharomyces cerevisiae strain S288C Genome Annotation Release R64.3.1 (April 2021)

• The S. cerevisiae strain S288C reference genome annotation was updated in its first major update since 2014. The new genome annotation is release R64.3, which released on April 21, 2021. Note that the underlying sequence of 16 assembled nuclear chromosomes, plus the mitochondrial genome, remained unchanged in annotation release R64.3.1 (relative to genome sequence release R64.2.1).

• This annotation update included:

  • 7 new ORFs: OTO1/YGR227C-A, YHR052C-B, YHR054C-B, YJR107C-A, YKL104W-A, YLR379W-A, YMR008C-A

  • 5 new ncRNAs: GAL10-ncRNA, TBRT/XUT_2F-154, SUT169, PHO84 lncRNA, GAL4 lncRNA

  • 2 new uORFs for ROK1/YGL171W

  • 1 new recombination enhancer: RE

  • 1 new LTR: YELWdelta27

  • 3 ORFs with shifted translation starts: HPA3/YEL066W, YJR012C, LTO1/YNL260C

  • 1 ORF with shifted translation stop plus new intron: LDO45/YMR147W

  • Changed feature_type (and SO_term) for non-transcribed spacers: NTS1-2, NTS2-1, NTS2-2

  • New systematic nomenclature system for entire annotated complement of ncRNAs

Saccharomyces cerevisiae strain S288C Genome Annotation Release R64.2.1 (November 2014)

• The underlying sequence of 16 assembled nuclear chromosomes, plus the mitochondrial genome, remained unchanged in annotation release R64.2.1 (relative to genome sequence release R64.1.1). The annotations of 2 existing proteins changed (GRX3/YDR098C and HOP2/YGL033W), and 1 new ORF (RDT1/YCL054W-A) and 4 RNAs (RME2, RME3, IRT1, ZOD1) were added to the genome annotation. Other additions include 8 nuclear matrix attachment sites, and 8 mitochondrial origins of replication. The coordinates of many autonomously replicating sequences (ARS) were updated, and many new ARS consensus sequences were added. Complete details can be found in the Summary of Chromosome Sequence and Annotation Updates.

• The R64.2.1 annotation release is submitted to GenBank and tracked with Assembly accession GCA_000146045.2. The identical assembly and annotation is copied into NCBI's RefSeq dataset, under Assembly accession GCF_000146045.2.

Systematic Sequencing Table

This table includes the following Saccharomyces cerevisiae chromosome statistics and retrieval options.

• Chromosome Region & Reference: Access to chromosome pages, and original sequencing project publications.

• DNA Coordinator: Contact information of the original Sequencing Coordinators for each chromosome.

• Total length: Current annotated length (in nucleotides base pairs) of each assembled chromosome sequence.

• S288c sub-strains(s): Actual strain (S288C or S288C-derivative) used in the original sequencing project.

• Retrieve: Links to various sequence and annotation retrieval options (JBrowse, SGD's Gene/Sequence Resources, and FASTA sequence files).

Go to Systematic Sequencing Table.

Chromosome pages

Each S288C Chromosome page currently includes two sections: Overview and Features.

The Overview section includes a pie chart depicting the relative portions of different types of genes and other chromosomal elements annotated on each chromosome. Also available are links to the S288C strain overview and NCBI chromosome record, as well as a button for downloading the chromosome sequence in FASTA format.

The Features section includes a visual representation of the chromosome map, and a sortable/filterable table listing all genes and other chromosomal elements annotated on that chromosome. Below the table are buttons that allow download of the table contents, or access to pre-loaded analysis tools (GO Term Finder, GO Slim Mapper, SPELL, YeastMine).

Go to ChrI | ChrII | ChrIII | ChrIV | ChrV | ChrVI | ChrVII | ChrVIII | ChrIX | ChrX | ChrXI | ChrXII | ChrXIII | ChrXIV | ChrXV | ChrXVI | ChrMito

Chromosome History

Please note: As of June 19, 2006, the Chromosome History replaces the "Table of Sequence Updates," the "Table of Sequence Annotation Changes," and all associated pages.

A table lists the number and dates of sequence and annotation changes to each chromosome. Each chromosome number is linked to the Chromosome History page for that chromosome.

At the top of each Chromosome History page are listed the numbers of sequence and annotation changes that have been made to the chromosome's systematic reference sequence since its intial release on 1996-07-31, as well as the number of chromosomal features that have been affected by these changes. Note that some changes may have affected more than one overlapping or adjacent feature, or some features may have been updated more than once, so that the number of changes may differ from the number of affected features. Also included is a link to the directory on SGD's Downloads site that contains current and archived versions of the chromosome's sequence and annotation records.

The Chromosome History contains the following two sections:

Sequence Changes, including any resulting annotation changes

This section displays SGD curator notes describing sequence changes that have been made to the chromosome's systematic reference sequence, as well as any annotation changes that resulted from those sequence changes.

Included above each note is a data row(s) containing information in the following columns:

• Date: the date the change was made

• Affected Features: names of the features affected by the change, hyperlinked to their respective Locus Summaries

• Start Coordinate of Change: the coordinate of the first nucleotide involved in the sequence change

• End Coordinate of Change: the coordinate of the last nucleotide involved in the sequence change

• Type of Change: the type of sequence change (deletion, insertion, or substitution)

• Old Sequence: the previous version of the sequence (pre-change)

• New Sequence: the updated version of the sequence (post-change)

The default sorting of the Sequence Change table is by Date with the most recent change at the top of the list. The column headings for Affected Features, Start Coordinate of Change, and Type of Change are clickable for ascending or descending sorting on those columns. The first click on each of these column headers will produce ascending sorting on that column, the second click will produce descending sorting, and subsequent clicks will alternate between the two.

Annotation Changes without sequence changes

This section displays SGD curator notes describing annotation changes that have been made to the chromosome, that specifically did NOT result from sequence changes. These types of changes can include the addition of a new feature, deletion of a feature, merge of one feature into another, a change in the annotated position of a start or stop codon, etc.

Included above each note is a data row(s) containing information in the following columns:

• Date: the date the change was made

• Affected Features: names of the features affected by the change, hyperlinked to their respective Locus Summaries

The default sorting of the Annotation Change table is by Date with the most recent change at the top of the list. The column heading for Affected Features is clickable for ascending or descending sorting on that column. The first click on this column header will produce ascending sorting, the second click will produce descending sorting, and subsequent clicks will alternate between the two.

Go to Chromosome Summary | Chromosome History