title: PLAZA 3.0: an access point for plant comparative genomics.
abstract: Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms.
authors.affiliation: University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Proost
authors.affiliation: VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium.
authors.forename: Michiel
authors.initials: M
authors.lastname: Van Bel
authors.affiliation: VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium.
authors.forename: Dries
authors.initials: D
authors.lastname: Vaneechoutte
authors.affiliation: VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium.
authors.forename: Dirk
authors.initials: D
authors.lastname: Inzé
authors.affiliation: University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Mueller-Roeber
authors.affiliation: VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium klaas.vandepoele@psb.vib-ugent.be.
authors.forename: Klaas
authors.initials: K
authors.lastname: Vandepoele
mesh_terms: D030541:Databases, Genetic; D019143:Evolution, Molecular; D018745:Genome, Plant; D023281:Genomics; D020407:Internet; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D010944:Plants / Q000145:classification / Q000235:genetics