PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes

  • Manuel Spannagl
  • Kai Bader
  • Matthias Pfeifer
  • Thomas Nussbaumer
  • Klaus F. X. MayerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1374)


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.

Key words

PlantsDB Wheat genome Barley genome GenomeZipper CrowsNest synteny browser 


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Manuel Spannagl
    • 1
  • Kai Bader
    • 1
  • Matthias Pfeifer
    • 1
  • Thomas Nussbaumer
    • 1
  • Klaus F. X. Mayer
    • 1
    • 2
    Email author
  1. 1.Plant Genome and Systems BiologyHelmholtz Center MunichNeuherbergGermany
  2. 2.School of Life Sciences WeihenstephanTechnical University MunichNeuherbergGermany

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