Gramene release 68 is out with new eFP Browsers, 150 plant genomes and a form to submit your gene's function!

The Gramene Knowledgebase Team is pleased to announce its Release #68, featuring 22 new reference plant genomes (including 15 rice cultivars, the IWGSC RefSeq v2.1 version of the bread wheat assembly and two new wheat cultivars, two oat genomes, and the ash tree genome) for a total of 150 plant reference genomes. In addition, the poplar assembly was updated from version 3 to 4, and teff was replaced with a new assembly. Functional annotations were updated for Japonica rice genes. This release features 156,836 gene family trees built from 3,867,457 protein coding genes spanning 110 of the plant genomes.

For this release, two new features in the search interface are:

1) For genes in trees, the closest annotated homolog (or model species homolog if the former was not found) is provided with percent identity.

2) For rice, maize, grapevine, and sorghum genes, a link for such gene in the corresponding pangenome site (i.e., Gramene Oryza, Gramene Maize, Gramene Vitis, and SorghumBase, respectively), is also provided. RNA-seq-based gene expression levels for curated Arabidopsis, maize, sorghum, and soybean genes in different expression datasets are now available through embedded eFP Browsers from the BAR.

In addition, a new form for users to submit a gene's function was embedded in the "Papers" tab of the search interface, see for example Os05g0421750 and click on the "Add Papers" instruction.

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 (USDA ARS 8062-21000-041-00D). 

Users and readers are encouraged to follow us @GrameneDatabase to get updates, highlights and news, through our integrated Twitter feed on Gramene’s homepage.