Virtualplant: A Software Platform for Translational Systems Biology Research in Crops

To enable Systems Biology studies across plant species, we have developed and expanded the VirtualPlant software platform to include Maize, Rice, Soy, and Arabidopsis genomes. VirtualPlant (www.virtualplant.org), originally developed for an NSF Arabidopsis 2010 Grant, includes tools for data analysis, integration and visualization such as the Arabidopsis MultiNetwork interaction database, as well as novel data visualization tools including BioMaps and Sungear [1,2]. VirtualPlant enables seamless integration of data and tools into a single software platform by virtue of its unique “Gene Cart”, which enables researchers to store results, enabling iterative cycles of analysis, a highlight of Systems Biology [3]. Additionally, VirtualPlant’s web-based user-friendly GUI enables plant biologists to analyze their own genomic data, enabling them to uncover and infer biological insights.

 VirtualPlant has played an integral part in enabling Plant Systems Biology research in Arabidopsis in prominent plant labs around the world.  Our recent expansion of VirtualPlant to include important crops such as Maize, Rice and Soy, facilitates the comparisons of crop networks to Arabidopsis, hence enabling translational research. For example, VirtualPlant allows researchers to predict how an interacting network of genes/products in crop genomes will react as a system in response to an environmental change or genetic modifications, and predict genes in the crop to target for manipulation.

 Here, we present a case study of how VirtualPlant can be used to enable hypothesis generation in Cassava by transferring “network knowledge” of gene interactions (e.g. protein-protein, protein-DNA, etc) from Arabidopsis.  Currently, VirtualPlant is cross-operational across Arabidopsis, Maize, Rice and Soy enabling translational network analysis. Additional crop genomes including Cassava, Brassica, Medicago, Grape, Tomato, Sorghum, and Poplar will be inducted into VirtualPlant in the near future.

[1] Katari, MS, Nowicki, SD, Aceituno, FF, Nero, D, Kelfer, J, Thompson, LP, Cabello, JM, Davidson, RS, Goldberg, AP, Shasha, DE, Coruzzi, GM, and Gutierrez, RA, VirtualPlant: a software platform to support systems biology research. Plant Physiol, 2010. 152(2): p. 500-515.

[2] Poultney, CS, Gutierrez, RA, Katari, MS, Gifford, ML, Paley, WB, Coruzzi, GM, and Shasha, DE, Sungear: interactive visualization and functional analysis of genomic datasets. Bioinformatics, 2007. 23(2): p. 259-261.

[3] Gutierrez, RA, Shasha, DE, and Coruzzi, GM, Systems biology for the virtual plant. Plant Physiol, 2005. 138(2): p. 550-554