Advertisement

WheatGenome.info: A Resource for Wheat Genomics Resource

  • Kaitao LaiEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1374)

Abstract

An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/.

Key words

Triticum aestivum Integrated database Comparative map Geneticmap Genomeviewer Second-generation DNA sequencing 

References

  1. 1.
    Brautigam A, Gowik U (2010) What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biol (Stuttg) 12(6):831–841CrossRefGoogle Scholar
  2. 2.
    Ansorge WJ (2009) Next-generation DNA sequencing techniques. N Biotechnol 25(4):195–203CrossRefPubMedGoogle Scholar
  3. 3.
    Edwards D, Batley J, Snowdon RJ (2013) Accessing complex crop genomes with next-generation sequencing. Theor Appl Genet 126(1):1–11CrossRefPubMedGoogle Scholar
  4. 4.
    Gupta PK, Mir RR, Mohan A, Kumar J (2008) Wheat genomics: present status and future prospects. Int J Plant Genomics 2008:896451PubMedCentralPubMedGoogle Scholar
  5. 5.
    Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubaláková M, Šimková H, Batley J, Fleury D, Doležel J, Edwards D (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
  6. 6.
    Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubalakova M, Simkova H, Batley J, Dolezel J, Hernandez P, Edwards D (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theor Appl Genet 124:423–432CrossRefPubMedGoogle Scholar
  7. 7.
    Berkman PJ, Visendi P, Lee HC, Stiller J, Manoli S, Lorenc MT, Lai K, Batley J, Fleury D, Simkova H, Kubalakova M, Weining S, Dolezel J, Edwards D (2013) Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnol J 11(5):564–571CrossRefPubMedGoogle Scholar
  8. 8.
    Somerville C (2006) The billion-ton biofuels vision. Science 312(5778):1277CrossRefPubMedGoogle Scholar
  9. 9.
    Draper J, Mur LA, Jenkins G, Ghosh-Biswas GC, Bablak P, Hasterok R, Routledge AP (2001) Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol 127(4):1539–1555PubMedCentralCrossRefPubMedGoogle Scholar
  10. 10.
    The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463(7282):763–768CrossRefGoogle Scholar
  11. 11.
    Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23(10):1282–1288CrossRefPubMedGoogle Scholar
  12. 12.
    Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Keeble-Gagnère G, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R, Fitzgerald A (2012) Bread matters: a national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnol J 10(6):703–708CrossRefPubMedGoogle Scholar
  13. 13.
    Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Muhindira PV, Ruperao P, Fitzgerald TL, Zander M, Chan C-KK, Manoli S, Stiller J, Batley J, Edwards D (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnol J 13(1):97–104CrossRefPubMedGoogle Scholar
  14. 14.
    Donlin MJ (2009) Using the Generic Genome Browser (GBrowse). Curr Protoc in Bioinformatics. Chapter 9 (Unit 9), 9Google Scholar
  15. 15.
    Arnaoudova EG, Bowens PJ, Chui RG, Dinkins RD, Hesse U, Jaromczyk JW, Martin M, Maynard P, Moore N, Schardl CL (2009) Visualizing and sharing results in bioinformatics projects: GBrowse and GenBank exports. BMC Bioinformatics 10, A4Google Scholar
  16. 16.
    Donlin M (2007) Using the Generic Genome Browser (GBrowse). Curr Protoc Bioinformatics. Chapter 9 (Unit 9), 9Google Scholar
  17. 17.
    Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J, Edwards D (2012) WheatGenome.info: an integrated database and portal for wheat genome information. Plant Cell Physiol 53(2), e2CrossRefPubMedGoogle Scholar
  18. 18.
    Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J, Edwards D (2010) Targeted identification of genomic regions using TAGdb. Plant Methods 6:19PubMedCentralCrossRefPubMedGoogle Scholar
  19. 19.
    Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7(1–2):203–214CrossRefPubMedGoogle Scholar
  20. 20.
    Youens-Clark K, Faga B, Yap IV, Stein L, Ware D (2009) CMap 1.01: a comparative mapping application for the Internet. Bioinformatics 25(22):3040–3042PubMedCentralCrossRefPubMedGoogle Scholar
  21. 21.
    Duran C, Boskovic Z, Imelfort M, Batley J, Hamilton NA, Edwards D (2010) CMap3D: a 3D visualisation tool for comparative genetic maps. Bioinformatics 26:273–274CrossRefPubMedGoogle Scholar
  22. 22.
    Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J, Edwards D (2009) AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Res 37:D951–D953PubMedCentralCrossRefPubMedGoogle Scholar
  23. 23.
    Duran C, Appleby N, Vardy M, Imelfort M, Edwards D, Batley J (2009) Single nucleotide polymorphism discovery in barley using autoSNPdb. Plant Biotechnol J 7(4):326–333CrossRefPubMedGoogle Scholar
  24. 24.
    Barker G, Batley J, O'Sullivan H, Edwards KJ, Edwards D (2003) Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19(3):421–422CrossRefPubMedGoogle Scholar
  25. 25.
    Batley J, Barker G, O'Sullivan H, Edwards KJ, Edwards D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 132(1):84–91PubMedCentralCrossRefPubMedGoogle Scholar
  26. 26.
    Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GAC, Mongin E, Barker G, Spangenberg GC, Edwards D (2005) SNPServer: a real-time SNP discovery tool. Nucleic Acids Res 33:W493–W495PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.School of Agriculture and Food ScienceUniversity of QueenslandSt. LuciaAustralia

Personalised recommendations