[Gramene-announce] Announcing Gramene knowledgebase release #63 with 26 new reference genomes

[Tello-Ruiz, Marcela]

Dear Plant Researchers,


The Gramene Knowledgebase Team is pleased to announce its Release #63<http://www.gramene.org/release-notes-63> with the Genome section<http://ensembl.gramene.org/genome_browser/index.html> providing access to information on 93 reference genomes and 122,947 gene family trees. We are adding 26 new reference genomes, including pineapple, cantaloupe, watermelon, Golden apple, clementine, sweet cherry, almond, pistachio, olive tree, cannabis or marijuana, tobacco, a relative of sugar cane, five varieties of European wheat, and new varieties of barley and cocoa. With these new genomes, our comparative genomics collection has reached a total of 382 pairwise DNA alignments and 84 synteny maps. We have also added SNP variation datasets for sunflower, Golden apple, and durum wheat.


The Plant Reactome<http://plantreactome.gramene.org/> is the pathway knowledgebase of Gramene. We utilize the Reactome pathway data model to represent plant metabolic, transport and signaling pathways, developmental processes, organ differentiation, and transcriptional regulatory networks. Manual biocuration is conducted in the reference species rice (O. sativa) and pathways are then projected via gene orthology to other species including crops and model plants, lower plants and single-cell photoautotrophs. In this release, we have extended orthology-based pathway projections for 9 new species; added 13 newly curated pathways; and updated 8 pathways in the reference species Oryza sativa.  In total, Plant Reactome is currently hosting  320 rice curated pathways and their gene-orthology based projection for 106 species ranging from unicellular autotrophs to higher plants.

The Gramene Knowledgebase is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. The genome databases were built in direct collaboration with Ensembl Plants and the Plant Reactome database was produced in collaboration with the 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 1907-21000-030-00D), and the National Science Foundation (NSF IOS-1127112<https://www.nsf.gov/awardsearch/showAward?AWD_ID=1127112>).

Please let us know if you have any questions or suggestions.

The Gramene Team<http://www.gramene.org/feedback>