GRCN-2013 Highlights

The Grape Research Coordination Network (GRCN)-2013 meeting was held in UC Davis, from July9-12, 2013.  About 70 participants including scientists, postdocs, graduate and undergraduate students attended this meeting.  Several groups in the grape community are generating high-throughput genomic data sets and need a bioinformatics infrastructure.  Several grape researchers use Gramene's genome portal, especially the grape genome browser and are very positive about the functionality of this portal. They view Gramene as a model database for organizing various genomic and genetic resources. Here is a brief update from the meeting.

New Genome assembly for Vitis vinifera: Stephane Rombauts (Ghent University, Belgium) is working on the new assembly of the Vitis vinifera genome that will be available soon. The new assembly is an improvisation of the previous 12x genome annotation.  The grape community is also working on the systematic nomenclature of Vitis vinifera genes. When it becomes available, Gramene will be able to update the Grape Genome portfolio.

Genome sequences of Grape cultivars: The Genome sequencing of many additional grape cultivars is being pursued.

Genomic Data sets: The community is producing huge amount of gene-expression data sets; RNA-Seq and micro-array, some of these are being deposited in the plexDB. There is ongoing discussion about the data formats and the necessary information that should be deposited in the public databases, so that comparisons can be made across data sets and studies done by various groups. Gramene can contribute in formulating some of these standard guidelines.

Metabolomics and Proteomics: The proteomic and metabolomic data sets for grape cultivars are increasingly being available in the  public domain. These data sets can provide an excellent support for improvisation of grape gene models and curation of grape genes, and grape metabolic and signaling pathways. Also this provides an opportunity to tap the secondary metabolites and novel compounds that are present in fleshy fruits and have not been curated earlier based on the information from the model organisms such as Arabidopsis and rice. Sushma Naithani from Oregon State University, presented VitisCyc database, a grape specific pathway database as a resource for organizing the grape metabolic networks and supporting the analysis of expression data sets.

Phenotyping grapevine in the context of climate change:
Prof. Serge Delrot talked about a database of digital images which consists of a collection of images grape cultivars and of specific plant parts from various regions and under diverse climates. This is a very important resource that can be connected with the genomic level expression data sets.