2018 ASHS Annual Conference

Gramene (http://www.gramene.org) is an integrated plant resource for reference genomes and comparative functional analysis in plants. Does your species have a reference assembly, transcript data or genetic variation data for entire populations? If so, these data sets may already be part of Gramene. The current Gramene release contains provides researchers with access to reference assemblies and annotation for 53 genomes (including peach, grape, banana, cocoa, cucumber, sugar beet, common bean, tomato, potato, cassava, yam, and Brassica crops) in a genome browser. In addition, we provide pathways views for 75 plants species including strawberry, orange, chili pepper, peas, and coffee, as well as the species listed above. Have you ever needed to know the function of the gene, and wanted to see the function of the ortholog in rice, maize or Arabidopsis? Does the gene you are working on belong to a large or small gene family. Did the gene family associated with expansion or contractions, in species that are evolutionary close? Is the biochemical pathway you work on conserved in sorghum and soybean? If so, Gramene can help you explore these questions in the Gramene. Gramene provides powerful phylogenetic approaches, including protein-based gene trees with stable IDs and whole-genome DNA alignments, enable traversing between plant species. We provide integrated search capabilities and interactive views to visualize gene features, gene neighborhoods, phylogenetic trees, genetic variation, gene expression profiles, pathways, and cross-references and host curated rice pathways, and uses these curated pathways to generate orthology-based projections for other species. Gramene builds upon Ensembl and Reactome software, and is committed to open accesses and reproducible science based on the FAIR principles, providing both human and machine access to the data. Gramene is supported by an NSF grant IOS-1127112, and from USDA-ARS (1907-21000-030-00D).