PlantSEED: A Resource for High-Throughput Comparison, Functional Annotation, and Metabolic Modeling of Plant Genomes

The impending flood of sequenced plant genomes demands a paradigm shift in how these genomes are analyzed, annotated, and used to develop predictive models. Today’s annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems we have developed PlantSEED (http://plantseed.theseed.org), an integrated, metabolism-centric database and toolkit that builds on the Arabidopsis thaliana and Zea mays genomes, and other genomes from Gramene. PlantSEED combines SEED subsystems technology, first developed for microbial genomes (Overbeek R et al, 2005, Nucleic Acids Res 33:5691-5702), with new protein family and biochemistry datasets to assign fully consistent functional annotations to orthologous metabolic genes, particularly those encoding primary metabolic pathways. Like its parent, the SEED database, PlantSEED incorporates a com­par­ative genome viewer and allows users to (re-)annotate genes. Crucially, the consistent annot­at­ions imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism in any plant. This opens the unique possibility of model-based assessment of the completeness and accur­acy of gene annotation, and thus to computational identify genes and pathways that are restricted to certain genomes or need better curation. Plant­SEED also features a tool to annotate plant genomes automat­ic­ally, starting from a full set of gene calls. We illustrate the potential of Plant­SEED by annotating two newly sequenced plant genomes (Malus domestica and Setaria italica) and by building models of primary metabolism for these species that highlight targets for further research.