Difference between revisions of "SGD Newsletter, Summer 2024"

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==Give a Gift / Support SGD==
 
==Give a Gift / Support SGD==
−
[[Image:gift.png |thumb|left|upright=.5]]
+
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]]
  
 
Budget cuts from NIH continue to strain SGD's finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. <i>Donations are now critical for our work to continue.</i>
 
Budget cuts from NIH continue to strain SGD's finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. <i>Donations are now critical for our work to continue.</i>
Line 9: Line 9:
 
Your generous gift to SGD will help us to continue providing essential information for your research and teaching efforts.  
 
Your generous gift to SGD will help us to continue providing essential information for your research and teaching efforts.  
  
−
To contribute, please make checks payable to Stanford University, noting that "the funds should be used to support the Saccharomyces Genome Database project, under the direction of Drs. Sherlock and Cherry in the Department of Genetics, Stanford University.  Account : GHJKO, Genetics : WAZC."  
+
To contribute, please make checks payable to Stanford University, noting that "the funds should be used to support the ''Saccharomyces'' Genome Database project, under the direction of Drs. Sherlock and Cherry in the Department of Genetics, Stanford University.  Account : GHJKO, Genetics : WAZC."  
  
 
Thank you for your support!
 
Thank you for your support!
Line 21: Line 21:
 
[mailto:sgd-helpdesk@lists.stanford.edu CONTACT US]: sgd-helpdesk@lists.stanford.edu
 
[mailto:sgd-helpdesk@lists.stanford.edu CONTACT US]: sgd-helpdesk@lists.stanford.edu
  
−
==Reference genome update R64.5 - still working on this one==
+
==Reference genome update R64.5==
 +
[[File:SuperYeast.jpg|link=https://www.yeastgenome.org|thumb|right|upright=.5]]
 
The ''S. cerevisiae'' strain S288C reference genome annotation has been updated to include previously unannotated features. 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.
 
The ''S. cerevisiae'' strain S288C reference genome annotation has been updated to include previously unannotated features. 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.
  
Line 33: Line 34:
 
Various sequence and annotation files are available on SGD’s [http://sgd-archive.yeastgenome.org Downloads] site. You can find more update details on the [https://wiki.yeastgenome.org/index.php/Details_of_2024_Reference_Genome_Annotation_Update_R64.5#R64.5_Annotation_update_summary Details of 2024 Reference Genome Annotation Update R64.5] SGD Wiki page.
 
Various sequence and annotation files are available on SGD’s [http://sgd-archive.yeastgenome.org Downloads] site. You can find more update details on the [https://wiki.yeastgenome.org/index.php/Details_of_2024_Reference_Genome_Annotation_Update_R64.5#R64.5_Annotation_update_summary Details of 2024 Reference Genome Annotation Update R64.5] SGD Wiki page.
  
−
==Extend gene coordinates in GFF==
+
==Extended gene coordinates in GFF==
 
The saccharomyces_cerevisiae.gff contains sequence features of ''Saccharomyces cerevisiae'' and related information such as Locus descriptions and GO annotations. The saccharomyces_cerevisiae.gff is fully compatible with [http://gmod.org/wiki/GFF3 Generic Feature Format Version 3], and is [http://sgd-archive.yeastgenome.org/curation/chromosomal_feature/ updated weekly].
 
The saccharomyces_cerevisiae.gff contains sequence features of ''Saccharomyces cerevisiae'' and related information such as Locus descriptions and GO annotations. The saccharomyces_cerevisiae.gff is fully compatible with [http://gmod.org/wiki/GFF3 Generic Feature Format Version 3], and is [http://sgd-archive.yeastgenome.org/curation/chromosomal_feature/ updated weekly].
  
−
After November 2020, SGD updated the transcripts in the GFF file to reflect the experimentally determined transcripts (Pelechano et al. 2013, Ng et al. 2020), when possible. The longest transcripts were determined for two different growth media – galactose and dextrose. When available, experimentally determined transcripts for one or both conditions were added for a gene. When this data was absent, transcripts matching the start and stop coordinates of an open reading frame (ORF) were used.
+
In recent years, SGD has made two significant changes to the GFF content (described in more detail below):
 +
*In November 2020, SGD updated the file to reflect experimentally determined transcripts
 +
*In February 2024, SGD edited the 'gene' entries in the file to extend the coordinates to encompass the start and stop coordinates of the longest experimentally determined transcripts
  
−
''Old version: BDH2/YAL061W with rows for longest transcripts expressed in GAL and in YPD.''
+
In November 2020, SGD updated the transcripts in the GFF file to reflect the experimentally determined transcripts (Pelechano et al. 2013, Ng et al. 2020), when possible. The longest transcripts were determined for two different growth media – galactose and dextrose. When available, experimentally determined transcripts for one or both conditions were added for a gene. When this data was absent, transcripts matching the start and stop coordinates of an open reading frame (ORF) were used.
 +
 
 +
''Starting November 2020: BDH2/YAL061W with rows for longest transcripts expressed in GAL and in YPD.''
 
[[File:yal061w_w2transcripts.jpg]]
 
[[File:yal061w_w2transcripts.jpg]]
  
−
Beginning in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition.  This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023).  
+
Then in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition.  This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023).  
  
 
''After February 2024: BDH2/YAL061W with expanded start/stop coordinates for 'gene', still with rows for longest transcripts expressed in GAL, YPD.''
 
''After February 2024: BDH2/YAL061W with expanded start/stop coordinates for 'gene', still with rows for longest transcripts expressed in GAL, YPD.''
 
[[File:yal061w_extendedgene.jpg]]
 
[[File:yal061w_extendedgene.jpg]]
  
−
This is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource.
+
GFF is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource.
  
−
==Updates to SGD search - still working on this one==
+
==Updates to SGD search==
−
datasets
+
[[File:sgd maintenanceguy.jpeg|link=https://www.yeastgenome.org/search?q=&is_quick=true|thumb|right|upright=.5]]
−
  complex aliases
+
SGD is jam-packed with information, with new data being added every day. It's a lot to keep up with, and with so much info, some inevitably ends up hidden from view. To make the various data types in SGD more readily accessible, we have made various improvements to the [https://www.yeastgenome.org/search?q=&is_quick=true SGD search]:
−
allele descriptions, SGDIDs
 
−
RNAcentral IDs
 
  
−
==PubTator link on SGD reference pages - still working on this one==
+
*New category for [https://www.yeastgenome.org/search?q=&category=dataset datasets]. Over 3700 yeast datasets are accessible. Search by reference, keyword, assay, and lab.
 +
*New Strains subcategory for [https://www.yeastgenome.org/search?q=&category=reference Reference] search. Scroll down to 'Associated Strains' in the lefthand menu on the Search Results page.
 +
*Macromolecular [https://www.yeastgenome.org/search?q=&category=complex complexes] can now be searched with aliases. Further refine by reference, subunit, function, process, and location.
 +
*Search for [https://www.yeastgenome.org/search?q=&category=allele alleles] via their descriptions and SGDIDs. Drill down based on reference, allele type, gene, and phenotype.
 +
*RNA products can now be searched using RNAcentral IDs.
  
 
==microPublications - latest yeast papers==
 
==microPublications - latest yeast papers==
−
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|https://www.micropublication.org|upright=.4]]
+
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]
  
 
[https://www.micropublication.org ​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 [https://pubmed.ncbi.nlm.nih.gov PubMed] and [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].  
 
[https://www.micropublication.org ​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 [https://pubmed.ncbi.nlm.nih.gov PubMed] and [https://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].  
Line 67: Line 74:
 
*[https://www.yeastgenome.org/reference/S000349401 Caligaris M, De Virgilio C (2024)] Proxies introduce bias in decoding TORC1 activity. MicroPubl Biol 2024.
 
*[https://www.yeastgenome.org/reference/S000349401 Caligaris M, De Virgilio C (2024)] Proxies introduce bias in decoding TORC1 activity. MicroPubl Biol 2024.
 
*[https://www.yeastgenome.org/reference/S000349402 Fromont-Racine M, Khanna V, Jacquier A, Badis G (2024)] YLR419W is the homolog of the mammalian translation initiation factor DHX29. MicroPubl Biol 2024.
 
*[https://www.yeastgenome.org/reference/S000349402 Fromont-Racine M, Khanna V, Jacquier A, Badis G (2024)] YLR419W is the homolog of the mammalian translation initiation factor DHX29. MicroPubl Biol 2024.
−
*[https://www.yeastgenome.org/reference/S000348700 Greenlaw A, Dell R, Tsukiyama T (2024)] Initial acidic media promotes quiescence entry in Saccharomyces cerevisiae. MicroPubl Biol 2024.
+
*[https://www.yeastgenome.org/reference/S000348700 Greenlaw A, Dell R, Tsukiyama T (2024)] Initial acidic media promotes quiescence entry in ''Saccharomyces cerevisiae''. MicroPubl Biol 2024.
 
*[https://www.yeastgenome.org/reference/S000348494 Harmer ZP, Hohener TC, Landolt AE, Mitchell C, McClean M (2024)] Enhancing high-throughput optogenetics: Integration of LITOS with Lustro enables simultaneous light stimulation and shaking. MicroPubl Biol 2024.
 
*[https://www.yeastgenome.org/reference/S000348494 Harmer ZP, Hohener TC, Landolt AE, Mitchell C, McClean M (2024)] Enhancing high-throughput optogenetics: Integration of LITOS with Lustro enables simultaneous light stimulation and shaking. MicroPubl Biol 2024.
−
*[https://www.yeastgenome.org/reference/S000347552 Karpel JE (2024) Caenorhabditis elegans ddx-15 helicase fails to complement loss of Prp43p in Saccharomyces cerevisiae. MicroPubl Biol 2024.
+
*[https://www.yeastgenome.org/reference/S000347552 Karpel JE (2024)] Caenorhabditis elegans ddx-15 helicase fails to complement loss of Prp43p in ''Saccharomyces cerevisiae''. MicroPubl Biol 2024.
 
*[https://www.yeastgenome.org/reference/S000347382 Medina-Suarez S, Machin F (2024)] The CRISPR/Cas9 system forms a condensate in the yeast nucleus. MicroPubl Biol 2024.
 
*[https://www.yeastgenome.org/reference/S000347382 Medina-Suarez S, Machin F (2024)] The CRISPR/Cas9 system forms a condensate in the yeast nucleus. MicroPubl Biol 2024.
−
*[https://www.yeastgenome.org/reference/S000348904 Putnam CD (2024)] Loss of mitochondrial DNA is associated with reduced DNA content variability in Saccharomyces cerevisiae. MicroPubl Biol 2024.
+
*[https://www.yeastgenome.org/reference/S000348904 Putnam CD (2024)] Loss of mitochondrial DNA is associated with reduced DNA content variability in ''Saccharomyces cerevisiae''. MicroPubl Biol 2024.
 
*[https://www.yeastgenome.org/reference/S000348874 Rosenbaum JC, Carlson AE (2024)] The SARS coronavirus accessory protein ORF3a rescues potassium conductance in yeast. MicroPubl Biol 2024.
 
*[https://www.yeastgenome.org/reference/S000348874 Rosenbaum JC, Carlson AE (2024)] The SARS coronavirus accessory protein ORF3a rescues potassium conductance in yeast. MicroPubl Biol 2024.
  
Line 77: Line 84:
  
 
==Alliance of Genome Resources - Latest Release 7.2==
 
==Alliance of Genome Resources - Latest Release 7.2==
−
[[Image:alliance_logo.png|thumb|right|https://www.alliancegenome.org|upright=.725]]
+
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]]
 
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort between SGD and other model organism databases (MODs), released [https://www.alliancegenome.org/release-notes version 7.2] in June 2024.
 
The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort between SGD and other model organism databases (MODs), released [https://www.alliancegenome.org/release-notes version 7.2] in June 2024.
  
−
The 7.2.0 release updates the Disease pages’ Associated Alleles table and the Associated Models table:
+
The 7.2.0 release updates the Associated Alleles and Associated Models tables on Disease pages:
  
 
*Each table has a new column, Disease Qualifier, with a working filter. The qualifier describes whether an allele or model may be, for example, implicated in the onset of a disease or a model for the severity of a disease, respectively
 
*Each table has a new column, Disease Qualifier, with a working filter. The qualifier describes whether an allele or model may be, for example, implicated in the onset of a disease or a model for the severity of a disease, respectively
Line 102: Line 109:
 
**June 24 to June 27, 2024
 
**June 24 to June 27, 2024
 
**Montanya Hotel & Lodge, Catalonia, Spain
 
**Montanya Hotel & Lodge, Catalonia, Spain
 +
*[https://meetings.cshl.edu/courses.aspx?course=C-YEAS&year=24 Yeast Genetics & Genomics]
 +
**July 23 to August 13, 2024
 +
**Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
 
*[https://www.pnwyc.net Pacific Northwest Yeast Club]
 
*[https://www.pnwyc.net Pacific Northwest Yeast Club]
 
**July 26, 2024
 
**July 26, 2024

Latest revision as of 10:56, 19 June 2024

About this newsletter:
This is the Summer 2024 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 view this newsletter as well as previous newsletters, on the SGD Community Wiki.

Give a Gift / Support SGD

gift.png

Budget cuts from NIH continue to strain SGD's finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. Donations are now critical for our work to continue.

Your generous gift to SGD will help us to continue providing essential information for your research and teaching efforts.

To contribute, please make checks payable to Stanford University, noting that "the funds should be used to support the Saccharomyces Genome Database project, under the direction of Drs. Sherlock and Cherry in the Department of Genetics, Stanford University.  Account : GHJKO, Genetics : WAZC."

Thank you for your support!

Kindly send by mail to:

Development Services
PO Box 20466
Stanford, CA 94309

CONTACT US: sgd-helpdesk@lists.stanford.edu

Reference genome update R64.5

SuperYeast.jpg

The S. cerevisiae strain S288C reference genome annotation has been updated to include previously unannotated features. 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.

The R64.5.1 update included:

Various sequence and annotation files are available on SGD’s Downloads site. You can find more update details on the Details of 2024 Reference Genome Annotation Update R64.5 SGD Wiki page.

Extended gene coordinates in GFF

The saccharomyces_cerevisiae.gff contains sequence features of Saccharomyces cerevisiae and related information such as Locus descriptions and GO annotations. The saccharomyces_cerevisiae.gff is fully compatible with Generic Feature Format Version 3, and is updated weekly.

In recent years, SGD has made two significant changes to the GFF content (described in more detail below):

  • In November 2020, SGD updated the file to reflect experimentally determined transcripts
  • In February 2024, SGD edited the 'gene' entries in the file to extend the coordinates to encompass the start and stop coordinates of the longest experimentally determined transcripts

In November 2020, SGD updated the transcripts in the GFF file to reflect the experimentally determined transcripts (Pelechano et al. 2013, Ng et al. 2020), when possible. The longest transcripts were determined for two different growth media – galactose and dextrose. When available, experimentally determined transcripts for one or both conditions were added for a gene. When this data was absent, transcripts matching the start and stop coordinates of an open reading frame (ORF) were used.

Starting November 2020: BDH2/YAL061W with rows for longest transcripts expressed in GAL and in YPD. yal061w w2transcripts.jpg

Then in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition. This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023).

After February 2024: BDH2/YAL061W with expanded start/stop coordinates for 'gene', still with rows for longest transcripts expressed in GAL, YPD. yal061w extendedgene.jpg

GFF is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource.

Updates to SGD search

sgd maintenanceguy.jpeg

SGD is jam-packed with information, with new data being added every day. It's a lot to keep up with, and with so much info, some inevitably ends up hidden from view. To make the various data types in SGD more readily accessible, we have made various improvements to the SGD search:

  • New category for datasets. Over 3700 yeast datasets are accessible. Search by reference, keyword, assay, and lab.
  • New Strains subcategory for Reference search. Scroll down to 'Associated Strains' in the lefthand menu on the Search Results page.
  • Macromolecular complexes can now be searched with aliases. Further refine by reference, subunit, function, process, and location.
  • Search for alleles via their descriptions and SGDIDs. Drill down based on reference, allele type, gene, and phenotype.
  • RNA products can now be searched using RNAcentral IDs.

microPublications - latest yeast papers

MicroPub.png

​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:

All yeast microPublications can be found in SGD.

Alliance of Genome Resources - Latest Release 7.2

alliance logo.png

The Alliance of Genome Resources, a collaborative effort between SGD and other model organism databases (MODs), released version 7.2 in June 2024.

The 7.2.0 release updates the Associated Alleles and Associated Models tables on Disease pages:

  • Each table has a new column, Disease Qualifier, with a working filter. The qualifier describes whether an allele or model may be, for example, implicated in the onset of a disease or a model for the severity of a disease, respectively
  • In addition to the Disease Qualifier, the Associated Models table now has new columns for Condition Modifier and Genetic Modifier
  • The “Annotation Details” pop-up has expanded to include more information.
    • Alleles table: Association, Genetic Modifiers, Genetic Sex, Notes, and Annotation Type
    • Models table: Genetic Sex, Notes, and Annotation Type
  • The Associated Models table now has working filters for the Experimental Condition, Condition Modifier, and Genetic Modifier columns, including the ability to filter on relationship (e.g. induced by) as well as content (e.g. “copper”)
  • The Download files from the disease page Associated Alleles table and Associated Models table now include additional information as well.
    • New columns and information for the Associated Alleles table include: Allele Association, Genetic Entity Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Genetic Sex, Notes, Annotation Type, Source URL, and Date.
    • New columns and information for the Associated Models table include: Model Type, Model Association, Disease Qualifier, Evidence Code Abbreviation, Experimental Conditions, Condition Modifiers, Genetic Modifier Relation, Genetic Modifier IDs, Genetic Modifier Names, Genetic Sex, Notes, Annotation Type, Source URL, and Date.

Upcoming conferences and courses

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