[Gramene-announce] Gramene release 66 is out with publications ascribed to curated genes

[Tello-Ruiz, Marcela]

Dear Plant Researchers,

The Gramene Knowledgebase Team is pleased to announce its Release #66<https://www.gramene.org/news> with 128 reference genomes and 152,102 gene family trees. We have added 10 new reference genomes including one tree (cork oak), two kinds of peas (common pea and cowpea or black-eyed pea), two grasses (rye grass and barnyard grass), rye, brown mustard, lemon-scented gum, and fonio millet (also known as hungry rice). Our comparative genomics collection<https://ensembl.gramene.org/info/genome/compara/compara_analyses.html> currently includes 278 pairwise DNA alignments and 79 synteny maps. All data is available for bulk download from Gramene’s FTP site<https://ftp.gramene.org/release-66/>.

In this release, we integrated gene functional annotations from NCBI's geneRIFs and rap-db's curated genes. Each of these curated sources provide a mapping between genes and publications, which are available from the Publications tab of the search results (see example<https://www.gramene.org/?filters=%7B%22status%22:%22init%22,%22operation%22:%22AND%22,%22negate%22:false,%22marked%22:false,%22leftIdx%22:0,%22rightIdx%22:3,%22children%22:[%7B%22fq_field%22:%22id%22,%22fq_value%22:%22Os09g0511900%22,%22name%22:%22Os09g0511900%22,%22category%22:%22Gene%22,%22leftIdx%22:1,%22rightIdx%22:2,%22negate%22:false,%22showMenu%22:false,%22marked%22:true%7D],%22showMarked%22:true,%22showMenu%22:false,%22moveCopyMode%22:%22%22,%22searchOffset%22:0,%22rows%22:20%7D&genomes=>). A total of 12,722 gene models now have associated publications which describe their function.

The homepage continues to include links to our crop specific pangenome sites for maize<https://maize-pangenome.gramene.org/>, rice<https://oryza.gramene.org/>, grapevine<https://vitis.gramene.org/> and sorghum<https://sorghumbase.org>. These pangenome sites provide access to additional genomes from the respective taxonomic clade for comparative analysis against the primary annotated reference genome representative. We have an integrated Twitter feed on the homepage through which users and readers are encouraged to follow us @GrameneDatabase<https://twitter.com/GrameneDatabase> to get updates, highlights and news.

The Plant Reactome<http://plantreactome.gramene.org/> is the pathway knowledgebase of Gramene. We use the Reactome pathway data model to curate and represent the reference plant metabolic, transport and signaling pathways, developmental processes, organ differentiation, and transcriptional regulatory networks. The pathway knowledgebase continues to host curated rice pathways and gene-orthology based projections for 120 species.

The Gramene Knowledgebase is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. The genome databases are a mirror of EMBL-EBI Ensembl Plants, and built in collaboration with Expression Atlas, and UniProt. The Plant Reactome database is produced in collaboration with the NIH-funded human Reactome project.

Core funding for the project is provided by the Agricultural Research Service of the U.S. Department of Agriculture<http://www.usda.gov/> (USDA ARS 8062-21000-041-00D).

The Gramene Team

Gramene website: https://www.sorghumbase.org

Contact us: <https://www.sorghumbase.org/contact> https://www.gramene.org/feedback

Release notes build 66: https://www.gramene.org/news<https://dev.gramene.org/main/v65/news>