VitisCyc: A Species-Specific Metabolic Pathway Database for Grape (Vitis vinifera)

Grapes are highly valued as fleshy fruits and for their products; raisins, juice, wine etc. The value of utilized grape production for United States alone for the year 2011 was estimated to be $ 4.293 billion (USDA 2012).  However, the changes in global climate are impacting the yields and the quality of grapes by exacerbating abiotic (cold temperature, drought, excessive soil moisture, change in photoperiod) and biotic (diseases) stress. The detailed knowledge of grape metabolism and how plant’s overall metabolism is affected by a variety of stress conditions is required to breed new varieties and/or to introduce appropriate changes in cultural practices within the existing vineyards. We have constructed VitisCyc: a grape-specific metabolic pathway database, based on sequenced genome for grapevine (Vitis vinifera), 'Pinot Noir' cultivar, with 12X annotations (provided by the International Grape Genome Program). Currently, VitisCyc harbors 54 super pathways which include 376 biosynthesis pathways, 34 catabolic pathways, 8 detoxification pathways, 37 energy related pathways and 7 transport pathways. The VitisCyc database and the analysis tools are available at http://palea.cgrb.oregonstate.edu:1555/jaiswallab/vitiscyc.shtml. Researchers can browse database for genes, enzymes, metabolites, and metabolic pathways, and using OMICs-viewer tool, can conduct analysis of their data. Here, we present an example, an analysis of a RNA-Seq data on berry development. We are improving the annotations of pathways using publicly available data and seek feedback/contribution from the grape research community to further improve this resource, innovate, and integrate new features.