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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)

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.

Key words

PlantsDB Wheat genome Barley genome GenomeZipper CrowsNest synteny browser 

References

  1. 1.
    Lobell DB, Schlenker W, Costa-Roberts J (2011) Climate trends and global crop production since 1980. Science 333(6042):616–620CrossRefPubMedGoogle Scholar
  2. 2.
    Godfray HCJ et al (2010) Food security: the challenge of feeding 9 billion people. Science 327(5967):812–818CrossRefPubMedGoogle Scholar
  3. 3.
    Matsumoto T et al (2005) The map-based sequence of the rice genome. Nature 436(7052):793–800CrossRefGoogle Scholar
  4. 4.
    Eilam T et al (2007) Genome size and genome evolution in diploid Triticeae species. Genome 50(11):1029–1037CrossRefPubMedGoogle Scholar
  5. 5.
    Wicker T et al (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell 23(5):1706–1718PubMedCentralCrossRefPubMedGoogle Scholar
  6. 6.
    Mochida K, Yamazaki Y, Ogihara Y (2004) Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol Genet Genomics 270(5):371–377CrossRefGoogle Scholar
  7. 7.
    Brenchley R et al (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491(7426):705–710PubMedCentralCrossRefPubMedGoogle Scholar
  8. 8.
    International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345(6194):1251788CrossRefGoogle Scholar
  9. 9.
    Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13(9):2178–2189PubMedCentralCrossRefPubMedGoogle Scholar
  10. 10.
    International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463(7282):763–768CrossRefGoogle Scholar
  11. 11.
    Paterson AH et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551–556CrossRefPubMedGoogle Scholar
  12. 12.
    International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436(7052):793–800CrossRefGoogle Scholar
  13. 13.
    Matsumoto T et al (2011) Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol 156(1):20–28PubMedCentralCrossRefPubMedGoogle Scholar
  14. 14.
    Altschul SF et al (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410CrossRefPubMedGoogle Scholar
  15. 15.
    Margulies M et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437(7057):376–380PubMedCentralPubMedGoogle Scholar
  16. 16.
    Miller JR, Koren S, Sutton G (2010) Assembly algorithms for next-generation sequencing data. Genomics 95(6):315–327PubMedCentralCrossRefPubMedGoogle Scholar
  17. 17.
  18. 18.
    Richter DC et al (2008) MetaSim: a sequencing simulator for genomics and metagenomics. PLoS One 3(10), e3373PubMedCentralCrossRefPubMedGoogle Scholar
  19. 19.
    Dolezel J et al (2012) Chromosomes in the flow to simplify genome analysis. Funct Integr Genomics 12(3):397–416PubMedCentralCrossRefPubMedGoogle Scholar
  20. 20.
    Luo MC et al (2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proc Natl Acad Sci U S A 110(19):7940–7945PubMedCentralCrossRefPubMedGoogle Scholar
  21. 21.
    Frank E et al (2004) Data mining in bioinformatics using Weka. Bioinformatics 20(15):2479–2481CrossRefPubMedGoogle Scholar
  22. 22.
    Gill BS et al (2004) A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics 168(2):1087–1096PubMedCentralCrossRefPubMedGoogle Scholar
  23. 23.
    Vrana J et al (2000) Flow sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). Genetics 156(4):2033–2041PubMedCentralPubMedGoogle Scholar
  24. 24.
    Vrana J et al (2012) Flow cytometric chromosome sorting in plants: the next generation. Methods 57(3):331–337CrossRefPubMedGoogle Scholar
  25. 25.
    Safar J et al (2010) Development of chromosome-specific BAC resources for genomics of bread wheat. Cytogenet Genome Res 129(1–3):211–223CrossRefPubMedGoogle Scholar
  26. 26.
    Choulet F et al (2014) Structural and functional partitioning of bread wheat chromosome 3B. Science 345(6194):1249721CrossRefPubMedGoogle Scholar
  27. 27.
    Berkman PJ et al (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol J 9(7):768–775CrossRefPubMedGoogle Scholar
  28. 28.
    Berkman PJ et al (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theor Appl Genet 124(3):423–432CrossRefPubMedGoogle Scholar
  29. 29.
    Ma J et al. (2013) Sequence-based analysis of translocations and inversions in bread wheat (Triticum aestivum L.). Plos One 8(11)Google Scholar
  30. 30.
    Hernandez P et al (2012) Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J 69(3):377–386CrossRefPubMedGoogle Scholar
  31. 31.
    Belova T et al (2013) Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat. BMC Genomics 14:222PubMedCentralCrossRefPubMedGoogle Scholar
  32. 32.
    Tanaka T et al (2014) Next-generation survey sequencing and the molecular organization of wheat chromosome 6B. DNA Res 21(2):103–114PubMedCentralCrossRefPubMedGoogle Scholar
  33. 33.
    Sears E, S.L. (1978) The telocentric chromosomes of common wheat. In: Proceedings of 5th international wheat genet symposium, 1978, p 389–407Google Scholar
  34. 34.
    Mayer KFX et al (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491(7426):711–6PubMedGoogle Scholar
  35. 35.
    Mochida K et al (2009) TriFLDB: a database of clustered full-length coding sequences from triticeae with applications to comparative grass genomics. Plant Physiol 150(3):1135–1146PubMedCentralCrossRefPubMedGoogle Scholar
  36. 36.
    Nussbaumer T et al (2013) MIPS PlantsDB: a database framework for comparative plant genome research. Nucleic Acids Res 41(Database issue):D1144–D1151PubMedCentralCrossRefPubMedGoogle Scholar
  37. 37.
    Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42(1):225–249CrossRefPubMedGoogle Scholar
  38. 38.
    Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30(7):1575–1584PubMedCentralCrossRefPubMedGoogle Scholar
  39. 39.
    Ling HQ et al (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496(7443):87–90CrossRefPubMedGoogle Scholar
  40. 40.
    Jia J et al (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496(7443):91–95CrossRefPubMedGoogle Scholar
  41. 41.
    Bolot S et al (2009) The ‘inner circle’ of the cereal genomes. Curr Opin Plant Biol 12(2):119–125CrossRefPubMedGoogle Scholar
  42. 42.
    Martis MM et al (2013) Reticulate evolution of the rye genome. Plant Cell 25(10):3685–3698PubMedCentralCrossRefPubMedGoogle Scholar
  43. 43.
    Mayer KF et al (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23(4):1249–1263PubMedCentralCrossRefPubMedGoogle Scholar
  44. 44.
    Mayer KF et al (2009) Gene content and virtual gene order of barley chromosome 1H. Plant Physiol 151(2):496–505PubMedCentralCrossRefPubMedGoogle Scholar
  45. 45.
    Pfeifer M et al (2013) The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics. Plant Physiol 161(2):571–582PubMedCentralCrossRefPubMedGoogle Scholar
  46. 46.
    Ashburner M et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29PubMedCentralCrossRefPubMedGoogle Scholar
  47. 47.
    Wilkinson MD, Links M (2002) BioMOBY: an open source biological web services proposal. Brief Bioinform 3(4):331–341CrossRefPubMedGoogle Scholar
  48. 48.
    Wilkinson M et al (2005) BioMOBY successfully integrates distributed heterogeneous bioinformatics Web Services. The PlaNet exemplar case. Plant Physiol 138(1):5–17PubMedCentralCrossRefPubMedGoogle Scholar
  49. 49.
    Stein LD et al (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12(10):1599–1610PubMedCentralCrossRefPubMedGoogle Scholar
  50. 50.
    Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111PubMedCentralCrossRefPubMedGoogle Scholar
  51. 51.
    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):511–515PubMedCentralCrossRefPubMedGoogle Scholar
  52. 52.
    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 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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