title: PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes.
abstract: PGSB (Plant Genome and Systems Biology; formerly MIPS-Munich Institute for Protein Sequences) has been involved in developing, implementing and maintaining plant genome databases for more than a decade. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable datasets for model plant genomes as a backbone against which experimental data, e.g., from high-throughput functional genomics, can be organized and analyzed. In addition, genomes from both model and crop plants form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny) between related species on macro- and micro-levels.The genomes of many economically important Triticeae plants such as wheat, barley, and rye present a great challenge for sequence assembly and bioinformatic analysis due to their enormous complexity and large genome size. Novel concepts and strategies have been developed to deal with these difficulties and have been applied to the genomes of wheat, barley, rye, and other cereals. This includes the GenomeZipper concept, reference-guided exome assembly, and "chromosome genomics" based on flow cytometry sorted chromosomes.
authors.affiliation: Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany.
authors.forename: Manuel
authors.initials: M
authors.lastname: Spannagl
authors.affiliation: Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany.
authors.forename: Kai
authors.initials: K
authors.lastname: Bader
authors.affiliation: Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Pfeifer
authors.affiliation: Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Nussbaumer
authors.affiliation: Plant Genome and Systems Biology, Helmholtz Center Munich, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany. k.mayer@helmholtz-muenchen.de.|School of Life Sciences Weihenstephan, Technical University Munich, 85354 Freising. 1, 85764, Neuherberg, Germany. k.mayer@helmholtz-muenchen.de.
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D006109:Poaceae / Q000235:genetics*; D064878:Web Browser
keywords: Barley genome; CrowsNest synteny browser; GenomeZipper; PlantsDB; Wheat genome