VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera)

Abstract

We have developed VitisCyc, a grapevine-specific metabolic pathway database that allows researchers to (i) search and browse the database for its various components such as metabolic pathways, reactions, compounds, genes and proteins, (ii) compare grapevine metabolic networks with other publicly available plant metabolic networks, and (iii) upload, visualize and analyze high-throughput data such as transcriptomes, proteomes, metabolomes etc. using OMICs-Viewer tool. VitisCyc is based on the genome sequence of the nearly homozygous genotype PN40024 of Vitis vinifera “Pinot Noir” cultivar with 12X v1 annotations and was built on BioCyc platform using Pathway Tools software and MetaCyc reference database. Furthermore, VitisCyc was enriched for plant-specific pathways and grape-specific metabolites, reactions and pathways. Currently VitisCyc harbors 68 super pathways, 362 biosynthesis pathways, 118 catabolic pathways, 5 detoxification pathways, 36 energy related pathways and 6 transport pathways, 10,908 enzymes, 2912 enzymatic reactions, 31 transport reactions and 2024 compounds. VitisCyc, as a community resource, can aid in the discovery of candidate genes and pathways that are regulated during plant growth and development, and in response to biotic and abiotic stress signals generated from a plant's immediate environment. VitisCyc version 3.18 is available online at http://pathways.cgrb.oregonstate.edu.

Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars

“…Each pathway summarizes abundance differences depicted as side-by-side heat maps that display the ratio of the individual cultivars average to the overall cultivars average abundance for each data point. The Omic data were overlaid onto customized metabolic pathway maps based upon annotated maps located at KEGG [ 50 ], PlantCyc [ 51 ], and VitisCyc [ 52 ]. Mapped enzymes without heat maps did not contain protein data.…”

Towards an open grapevine information system

“…Another interesting effort is The Metabolomics Workbench 44 (http://metabolomicsworkbench.org/) that aims at delivering a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials and training material. In parallel, a grapevine-specific metabolic pathway database was developed using hierarchical schema based on gene ontology and enzyme function (VitisCYC 45 ). But these efforts need to be more widely promoted within the grapevine community as only five experiments from two laboratories and related to Vitis vinifera have been deposited so far in MetaboLights (two related to living tissues and three from wine extracts).…”

“…It is the responsibility of these groups to publish well-formatted data sets with complete metadata and well described measured variables to the second category of contributors, the data repositories. These vary from generically focused, international efforts (for example, Genesys for genetic resources, EMBL and NCBI archives for various genomic data, see Figure 3) to smaller, community-maintained repositories, focused on grapevine-specific problems or national datasets 32,45,47–50 (Figure 3). …”

FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca

“…Using both methods, we provided preliminary annotations and GO assignments to 25,050 polypeptides. Similar methods have been employed earlier for the construction of RiceCyc (Dharmawardhana et al, 2013 ), MaizeCyc (Monaco et al, 2013 ), and VitisCyc (Naithani et al, 2014 ).…”

“…Due to the common underlying platform, exchange of relevant information between FragariaCyc and other BioCyc databases is greatly facilitated. Also, users can make quick cross-species comparisons of pathways, compounds, reactions, genes, and gene products with other publicly available BioCyc databases including AraCyc ( Arabidopsis thaliana ) (Mueller et al, 2003 ), RiceCyc ( Oryza sativa ) (Dharmawardhana et al, 2013 ), MedicCyc ( Medicago truncatul a) (Urbanczyk-Wochniak and Sumner, 2007 ), MaizeCyc ( Zea mays ) (Monaco et al, 2013 ), PoplarCyc ( Populus trichocarpa ) (Zhang et al, 2010 ), VitisCyc ( Vitis vinifera ) (Naithani et al, 2014 ), etc. BioCyc databases also provide built-in tools for carrying out gene-expression analysis and flux balance analysis.…”