Plant Genomics Databases pp 33-44

Part of the Methods in Molecular Biology book series (MIMB, volume 1533)

| Cite as

PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data

  • Manuel Spannagl
  • Thomas Nussbaumer
  • Kai Bader
  • Heidrun Gundlach
  • Klaus F. X. Mayer
Protocol

Abstract

Plant Genome and Systems Biology (PGSB), formerly Munich Institute for Protein Sequences (MIPS) PlantsDB, is a database framework for the integration and analysis of plant genome data, developed and maintained for more than a decade now. Major components of that framework are genome databases and analysis resources focusing on individual (reference) genomes providing flexible and intuitive access to data. Another main focus is the integration of genomes from both model and crop plants to form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny). Data exchange and integrated search functionality with/over many plant genome databases is provided within the transPLANT project.

Key words

PlantsDB Plant genome database Triticeae genomes GenomeZipper CrowsNest synteny browser transPLANT 

References

  1. 1.
    Ashburner M et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Bolser D et al (2016) Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomics data. Methods Mol Biol 1374:115–140CrossRefPubMedGoogle Scholar
  3. 3.
    Stein LD et al (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12(10):1599–1610CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Lamesch P et al (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40(Database issue):D1202–D1210CrossRefPubMedGoogle Scholar
  5. 5.
    Tomato Genome C (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635–641CrossRefGoogle Scholar
  6. 6.
    Altschul SF et al (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410CrossRefPubMedGoogle Scholar
  7. 7.
    International Wheat Genome Sequencing, C (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345(6194):1251788CrossRefGoogle Scholar
  8. 8.
    Ling HQ et al (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496(7443):87–90CrossRefPubMedGoogle Scholar
  9. 9.
    Jia J et al (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496(7443):91–95CrossRefPubMedGoogle Scholar
  10. 10.
    International Barley Genome Sequencing, C et al (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491(7426):711–716Google Scholar
  11. 11.
    Brenchley R et al (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491(7426):705–710CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Martis MM et al (2013) Reticulate evolution of the rye genome. Plant Cell 25(10):3685–3698CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Mascher M et al (2013) Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J 76(4):718–727CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Mayer KF et al (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23(4):1249–1263CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Moore G et al (1995) Cereal genome evolution. Grasses, line up and form a circle. Curr Biol 5(7):737–739CrossRefPubMedGoogle Scholar
  16. 16.
    Mayer KF et al (2009) Gene content and virtual gene order of barley chromosome 1H. Plant Physiol 151(2):496–505CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Trapnell C et al (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511–515CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Nussbaumer T et al (2014) RNASeqExpressionBrowser--a web interface to browse and visualize high-throughput expression data. Bioinformatics 30(17):2519–2520CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Manuel Spannagl
    • 1
  • Thomas Nussbaumer
    • 1
  • Kai Bader
    • 1
  • Heidrun Gundlach
    • 1
  • Klaus F. X. Mayer
    • 1
  1. 1.Plant Genome and Systems BiologyHelmholtz Center MunichNeuherbergGermany

Personalised recommendations