SGD Newsletter, Spring 2021

About this newsletter:

This is the Summer 2021 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. You can also subscribe to SGD's RSS feed to receive updates on SGD news: http://www.yeastgenome.org/feed

R64.3 Annotation Update

SGD curators periodically update the chromosomal annotations of the S. cerevisiae Reference Genome, which is derived from strain S288C.

The R64.3 annotation release included various updates and additions:

• 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

Various sequence and annotation files are available on SGD's Downloads site. You can find more update details and see the new systematic nomenclature system for noncoding RNA genes on the Details of 2021 Reference Genome Annotation Update R64.3 SGD Wiki page.

YeastMine Updates and New Templates

SGD has updated the current Gene-->UTRs template with newly calculated 5' and 3' UTR sequence/coordinates. We have also added a new template for Transcripts based on the data from the Pelachano et al 2013 study.

Textpresso Update

Textpresso has recently been updated with a new system, bringing an overhauled user interface and new features. The updated Textpresso still allows users to search the corpus of texts with specialized queries using keywords and related categories, but now search results are shown in the context of the full text. For more information about the changes and types of papers stored in Textpresso, please read their About Us help section.

Fungal Pathogen Genomics Workshop

From May 10th - 14th, Senior Biocuration Scientist Edith Wong, Senior Biocuration Scientist Rob Nash, Senior Biocuration Scientist Marek Skrzypek, Biocuration Scientist Suzi Aleksander, and Associate Biocuration Scientist Micheal Alexander attended the Fungal Pathogen Genomics Workshop. SGD Curators helped attendees learn more about using the unique tools on our website and were able to interact with curators from other fungal databases at FungiDB, EnsemblFungi, PomBase, CGD, MycoCosm, and JGI.

We would like to thank the Fungal Pathogen Genomics team for hosting a fun and successful virtual workshop for experimental biologists to gain valuable experience!

insert picture to the left of text

New Homology Pages

SGD is excited to introduce our new Homology Pages! These pages can be accessed by clicking on the Homology tab in the header of SGD gene pages, as seen below.

insert picture later

The information displayed on the Homology Pages is divided into several sections:

• Homologs: Information about known homologs for the gene of interest, such as the species of the homolog, the corresponding Gene ID from the Alliance of Genome Resources, and the name of the homolog.
• Functional Complementation: Data about cross-species functional complementation between yeast and other species, curated by SGD and the Princeton Protein Orthology Database (P-POD).
• Fungal Homologs: Curated homolog information for 24 additional species of fungi. View the species of the fungal homolog, the database source of the entry, and the Gene ID of the homolog from that database.
• External Identifiers: A list of external identifiers for the protein from various database sources.

insert picture

Functional Complementation Data Available on References Pages

References with curatable functional complementation data now display this information on the corresponding reference page. This data describes cross-species functional complementation between yeast and other species, and is curated by SGD and the Princeton Protein Orthology Database (P-POD).

insert picture

More Alleles

SGD now has almost 13,000 alleles that are either fully or partially curated. You can view all the alleles in our database by using the corresponding YM template or search for a specific allele in the website search bar.

picture of search with allele count? allele page? no pic?