Plant and Animal Genome XXV Conference

January 13 - 18, 2017

4231

Gramene Database: A resource for comparative plant genomics, pathways and phylogenomics analyses

The Gramene database (http://www.gramene.org) is an integrated resource for comparative genomics, phylogenetic and pathway analysis in plants. The database provides agricultural researchers and plant breeders with valuable biological information on genomes and plant pathways of numerous crops and model species, thus enabling powerful comparisons across species. During this workshop, we will demonstrate how to navigate the website and review the available resources at Gramene, including an improved search tool and web interface that allows users to interpret and explore queried data, a Genome Browser with 44 plant reference genomes, newly curated pathways and orthologous pathway projections in the Plant Reactome, and integrated plant gene expression data from Expression Atlas. In addition, we will showcase the power of Gramene's resources for mining rice disease resistance genes and performing a transcriptome analysis of salinity response in rice. This workshop is open to the community of plant researchers and breeders; beginners, as well as frequent users of the Gramene database alike are welcome and encouraged to join. Attendees may bring their own data to work with during the workshop. The current data release of Gramene includes the reference genomes and corresponding gene annotations for plant species including rice, maize, wheat, barley, soybean, Arabidopsis, Brassicas, medicago, tomato, potato, beet, banana, cocoa, peach, grapevine, poplar, red clover, Amborella, spikemoss and algae. In addition to ~240 curated reference rice pathways, the Plant Reactome incorporates pathway projections to 66 plant species, including the above 44, wild peanut ancestors and the common bean.