The DOE Systems Biology Knowledgebase (KBase): Progress Towards Advanced Modeling of Sustainable Bioenergy Crop Development

The U.S. Department of Energy Systems Biology Knowledgebase (KBase, http://kbase.us) aims to provide an open platform for comparative functional genomics and system biology research on microbes, plants and their communities, and for sharing results and methods between scientists.

 KBase provides a variety of plant resources and analytical services that are integrated with gene expression profiles, regulatory interactions, and metabolic networks. For example, users can run RNA-seq pipeline and tools for downstream analysis to quantify expression from the RNA-seq reads, perform transcriptome assembly, gene annotation and identify differential expression between tissues, developmental stages, environmental conditions and genetic backgrounds.

 KBase also enables the construction and curation of metabolic models of specific microbes, fungal, and plant genomes and their interactions, to understand plant microbial and mycorrhizal interactions, and generate new hypotheses such as metabolic reconstruction and flux balance analyses simulations using the expression matrix to generate the set of reactions active in biomass production.

 To learn more about using KBase to reconstruct metabolic models for plants and microbial interactions, start with the Featured Narrative titled Cyanobacteria-Sphagnum Metabolic Interactions (https://narrative.kbase.us/narrative/ws.9667.obj.2) a self-contained tutorial concerning Sphagnum (Peat Moss, Bryophyta) and Anabaena (N2-fixing diazotrophs, Cyanobacteria) that includes annotating the plant and microbial genomes with metabolic functions, reconstructing and gapfilling metabolic models using appropriately composed media, and then merging the two models into a community model which exhibits nitrogen fixation and exchange. This knowledge can then be applied to discover and develop novel biological constructs to improve biomass quality trait for biofuels.