New & Noteworthy

Reference Genome Annotation Update R64.2.1

February 23, 2015

SGD curators periodically update the chromosomal annotations of the S. cerevisiae Reference Genome, which is derived from strain S288C. Last November, the genome annotation was updated for the first time since the release of the major S288C resequencing update in February 2011. Note that 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 R64.2.1 annotation release included various updates and additions. 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.

New Protein Modification and Abundance Data in YeastMine

December 17, 2014

Have you ever wondered what’s happening to your favorite protein as it’s hanging out in the cell? SGD’s advanced search tool, YeastMine, now includes four new templates that can be used to find protein modification and abundance data.

The Gene -> Protein Modifications template retrieves phosphorylation, ubiquitination, succinylation, acetylation and methylation data, currently curated from the following 11 publications: Peng et al. 2003, Hitchcock et al. 2003, Seyfried et al. 2008, Vogtle et al. 2009, Ziv et al. 2011, Mommen et al. 2012, Henriksen et al. 2012, Swaney et al. 2013, Kolawa et al. 2013, Weinert et al. 2013, and Wang et al. 2014.

The Gene -> Experimental N-termini and N-terminal modifications template retrieves experimentally-determined amino-terminal sequence and acetylation data, currently curated from Vogtle et al. 2009 and Mommen et al. 2012.

Lastly, two new templates pull protein abundance data curated from Ghaemmaghami et al. 2003. Gene -> Protein Abundance retrieves molecules/cell counts for a gene or list of genes. The same data can be quickly filtered using the Retrieve -> Proteins in a given molecules/cell abundance range template.

Please explore these new YeastMine protein data templates, and send us your feedback.

New Alternative Reference Genomes

December 8, 2014

At SGD, we are expanding our scope to provide annotation and comparative analyses of all major budding yeast strains, and are making progress in our move toward providing multiple reference genomes. To this end, the following new S. cerevisiae genomes have been incorporated into SGD as “Alternative References”: CEN.PK, D273-10B, FL100, JK9-3d, RM11-1a, SEY6210, SK1, Sigma1278b, W303, X2180-1A, Y55. These genomes are accessible via Sequence, Strain, and Contig pages, and are the genomes for which we have curated the most phenotype data, and for which we aim to curate specific functional information. It is important to emphasize that we are not abandoning a standard sequence; S288C is still in place as “The Reference Genome”. However, we do recognize that it is helpful for students and researchers to be able to ‘shift the reference’, selecting the genome that is most appropriate and informative for a specific area of study.

These new genome sequences have been also been added to SGD’s BLAST datasets, multiple sequence alignments, the Pattern Matching tool, and the Downloads site. Please explore these new genomes, and send us your feedback.

New Sequence, Chromosome, and Contig pages

August 25, 2014

New Sequence pages are now available in SGD for virtually every yeast gene (e.g., HMRA1 Sequence page), and include genomic sequence annotations for the Reference Strain S288C, as well as several Alternative Reference Genomes from strains such as CEN.PK, RM11-1a, Sigma1278b, and W303 (more Alternative References coming soon). Each page includes an Overview section containing descriptive information, maps depicting genomic context in Reference Strain S288C (as shown below) and Alternative Reference strains, as well as chromosomal and relative coordinates in S288C.

The sequence itself includes display options for genomic DNA, coding DNA, or translated protein.

Also available on each Sequence page are links to redesigned S288C Chromosome pages, links to new Contig pages for Alternative Reference Genomes, and a Downloads menu for easy access to DNA sequences of several other industrial strains and environmental isolates. The new Sequence, Chromosome, and Contig pages make use of many of the features you enjoy on other new or redesigned pages at SGD, including graphical display of data, sortable tables, and responsive visualizations. The Sequence pages also provide seamless access to other tools at SGD such as BLAST and Web Primer. Please explore these new pages, accessible via the Sequence tab on your favorite Locus Summary page, and send us your feedback.

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