Gramene release 65 is out with a new CLIMtools portal

The Gramene Knowledgebase Team is pleased to announce its Release #65 with 118 reference genomes and 124,010 gene family trees. We are adding 4 new reference genomes (hazelnut, common fig, lettuce, and domesticated variety of the European olive tree), and replacing the Chiifu-401-42 cultivar of Brassica rapa with cultivar R-o-18. We are also updating the assemblies of barley and sunflower, and the gene annotations for barley, Chlamydomonas reinhardtii, and wheat cultivars. Our comparative genomics collection currently includes 320 pairwise DNA alignments and 80 synteny maps. Other updates include additional SIFT predictions, repeat masking using Repeat Detector (Red), and centromere data specifically added to wheat. All data is available for bulk download from Gramene’s FTP site.

In this release, we are introducing the CLIMtools portal that brings interactive web-based views of environment x genome associations, RiboSNitch prediction, and correlations between the local environment and a pool of curated phenotypes. In addition, we present an improved look and feel of the homepage and gene search interface. The homepage now includes links to our crop specific pangenome sites for maize, rice, grapevine and sorghum. 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 now integrated a Twitter feed on the homepage. Users and readers are encouraged to follow us @GrameneDatabase to get updates, highlights and news.

The Plant Reactome 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. This release is a maintenance release, except that Plant Reactome cross-references were added to individual maize genes in the Ensembl genome browser. The pathway knowledgebase continues to host 320 curated rice pathways and gene-orthology based projections for 120 species. The 12 new species with pathway projections include quinoa, muskmelon, fig, English walnut, loose-leaf lettuce, blue pigmy lily, olive, opium poppy, China rose, sesame, and green foxtail millet.

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).