title: High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.
abstract: The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. 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 the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for cross-kingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of model-based assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed.
authors.affiliation: Mathematics and Computer Science Division andComputation Institute, The University of Chicago, Chicago, IL 60637;
authors.forename: Samuel M D
authors.initials: SM
authors.lastname: Seaver
authors.affiliation: Mathematics and Computer Science Division andFellowship for Interpretation of Genomes, Burr Ridge, IL 60527;
authors.forename: Svetlana
authors.initials: S
authors.lastname: Gerdes
authors.affiliation: Horticultural Sciences Department and.
authors.forename: Océane
authors.initials: O
authors.lastname: Frelin
authors.affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611;
authors.forename: Claudia
authors.initials: C
authors.lastname: Lerma-Ortiz
authors.affiliation: Horticultural Sciences Department and.
authors.forename: Louis M T
authors.initials: LM
authors.lastname: Bradbury
authors.affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611;
authors.forename: Rémi
authors.initials: R
authors.lastname: Zallot
authors.affiliation: Horticultural Sciences Department and.
authors.forename: Ghulam
authors.initials: G
authors.lastname: Hasnain
authors.affiliation: Horticultural Sciences Department and.
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Niehaus
authors.affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611;
authors.forename: Basma
authors.initials: B
authors.lastname: El Yacoubi
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; and.
authors.forename: Shiran
authors.initials: S
authors.lastname: Pasternak
authors.affiliation: Mathematics and Computer Science Division andComputation Institute, The University of Chicago, Chicago, IL 60637;
authors.forename: Robert
authors.initials: R
authors.lastname: Olson
authors.affiliation: Computation Institute, The University of Chicago, Chicago, IL 60637;Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527;Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, IL 60439;
authors.forename: Gordon
authors.initials: G
authors.lastname: Pusch
authors.affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527;
authors.forename: Ross
authors.initials: R
authors.lastname: Overbeek
authors.affiliation: Computation Institute, The University of Chicago, Chicago, IL 60637;Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, IL 60439;
authors.forename: Rick
authors.initials: R
authors.lastname: Stevens
authors.affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611;
authors.forename: Valérie
authors.initials: V
authors.lastname: de Crécy-Lagard
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; andUS Department of Agriculture-Agricultural Research Service North Atlantic Area Plant, Soil and Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY 14853.
authors.forename: Doreen
authors.initials: D
authors.lastname: Ware
authors.affiliation: Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527;
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Hanson
authors.affiliation: Mathematics and Computer Science Division andComputation Institute, The University of Chicago, Chicago, IL 60637; chenry@mcs.anl.gov.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Henry
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008954:Models, Biological; D058977:Molecular Sequence Annotation / Q000379:methods*; D010944:Plants / Q000235:genetics* / Q000378:metabolism; D012984:Software; D049490:Systems Biology / Q000379:methods
keywords: computational biochemistry; plant genomics; plant metabolism; systems biology