Journal of Wood Science

, Volume 55, Issue 6, pp 395–400 | Cite as

A database for poplar gene co-expression analysis for systematic understanding of biological processes, including stress responses

  • Yoshiyuki Ogata
  • Hideyuki Suzuki
  • Daisuke Shibata
Original Article


Reforestation in the humid tropics and arid zones, where trees are often subject to stresses, is an effective approach for mitigating global warming. Forestation with Populus species that are tolerant to the stresses in such regions has been conducted. The selection of poplar trees with higher stress tolerance leads to more efficient reforestation. The genome-wide bioinformatics approaches of gene function have been used for revealing the mechanisms of biological processes, including such stress tolerance. The decoding of the poplar genome has been followed by the genome-wide identification of genes and then the inference of gene function for systematic understanding of biological processes. To predict gene function in poplar, we analyzed poplar gene expression data using DNA microarray datasets obtained from the Gene Expression Omnibus database and developed a database for poplar gene co-expression analysis. Using the database, we illustrate the steps to retrieve two groups of co-expressed genes that are specifically expressed in experiments of hypoxic stress response in gray poplar, a flooding-tolerant tree species. Our database allows users to extract genes involved in biological processes, such as stress reaction, and then is useful for understanding such mechanisms in tree species.

Key words

Co-expression Database Poplar Biological processes DNA microarray 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Bonan GB (2008) Forests and climate change: forcings, feedbacks, and the climate benefi ts of forests. Science 320:1444–1449CrossRefPubMedGoogle Scholar
  2. 2.
    Brosché M, Vinocur B, Alatalo ER, Lamminmäki A, Teichmann T, Ottow EA, Djilianov D, Afi f D, Boteat-Triboulot MB, Altman A, Polle A, Dreyer E, Rudd S, Paulin L, Auvinen P, Kangasjärvi J (2005) Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert. Genome Biol 6(12): R101CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Bogeat-Triboulot MB, Brosché M, Renaut J, Jouve L, Le Thiec D, Fayyaz P, Vinocur B, Witters E, Laukens K, Teichmann T, Altman A, Hausman JF, Polle A, Kangasjärvi J, Dreyer E (2007) Gradual soil water depletion results in reversible changes of gene expression, protein profiles, ecophysiology, and growth performance in Populus euphratica, a poplar growing in arid regions. Plant Physiol 143(2):876–892CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Xu X, Yang F, Xiao X, Zhang S, Korpelainen H, Li C (2008) Sex-specific responses of Populus cathayana to drought and elevated temperatures. Plant Cell Environ 31(6):850–860CrossRefPubMedGoogle Scholar
  5. 5.
    Xiao X, Yang F, Zhang S, Korpelainen H, Li C (2009) Physiological and proteomic responses of two contrasting Populus cathayana populations to drought stress. Physiol Plant 136(2):150–168CrossRefPubMedGoogle Scholar
  6. 6.
    Renaut J, Lutts S, Hoffmann L, Hausman JF (2004) Responses of poplar to chilling temperatures: proteomic and physiological aspects. Plant Biol (Stuttg) 6(1):81–90CrossRefGoogle Scholar
  7. 7.
    Guo XH, Jiang J, Lin SJ, Wang BC, Wang YC, Liu GF, Yang CP (2009) A ThCAP gene from Tamarix hispida confers cold tolerance in transgenic Populus (P. davidiana x P. bolleana) Biotechnol Lett 31(7):1079–1087CrossRefPubMedGoogle Scholar
  8. 8.
    Kreuzwieser J, Hauberg J, Howell KA, Carroll A, Rennenberg H, Millar AH, Whelan J (2009) Differential responses of gray poplar leaves and roots underpins stress adaptation during hypoxia. Plant Physiol 149(1):461–473CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Ferreira S, Hjernø K, Larsen M, Wingsle G, Larsen P, Fey S, Roepstorff P, Salomé Pais M (2006) Proteome profiling of Populus euphratica Oliv. upon heat stress. Ann Bot (Lond) 98(2):361–377CrossRefGoogle Scholar
  10. 10.
    Street NR, Skogström O, Sjödin A, Tucker J, Rodríguez-Acosta M, Nilsson P, Jansson S, Taylor G (2006) The genetics and genomics of the drought response in Populus. Plant J 48(3):321–341CrossRefPubMedGoogle Scholar
  11. 11.
    Plomion C, Lalanne C, Claverol S, Meddour H, Kohler A, Bogeat-Triboulot MB, Barre A, Le Provost G, Dumazet H, Jacob D, Bastien C, Dreyer E, de Daruvar A, Guehl JM, Schmitter JM, Martin F, Bonneu M (2006) Mapping the proteome of poplar and application to the discovery of drought-stress responsive proteins. Proteomics 6(24):6509–6527CrossRefPubMedGoogle Scholar
  12. 12.
    Rizzo M, Bernardi R, Salvini M, Nali C, Lorenzini G, Durante M (2007) Identification of differentially expressed genes induced by ozone stress in sensitive and tolerant poplar hybrids. J Plant Physiol 164(7):945–949CrossRefPubMedGoogle Scholar
  13. 13.
    Caruso A, Chefdor F, Carpin S, Depierreux C, Delmotte FM, Kahlem G, Morabito D (2008) Physiological characterization and identification of genes differentially expressed in response to drought induced by PEG 6000 in Populus canadensis leaves. J Plant Physiol 165(9):932–941CrossRefPubMedGoogle Scholar
  14. 14.
    Souza Cde A, Barbazuk B, Ralph SG, Bohlmann J, Hamberger B, Douglas CJ (2008) Genome-wide analysis of a land plant-specific acyl:coenzyme A synthetase (ACS) gene family in Arabidopsis, poplar, rice and Physcomitrella. New Phytol 179(4):987–1003PubMedGoogle Scholar
  15. 15.
    Kieffer P, Planchon S, OUfir M, Ziebel J, Dommes J, Hoffmann L, Hausman JF, Renaut J (2009) Combining proteomics and metabolite analyses to unravel cadmium stress-response in poplar leaves. J Proteome Res 8(1):400–417CrossRefPubMedGoogle Scholar
  16. 16.
    Azaiez A, Boyle B, Levée V, Séguin A (2009) Transcriptome profiling in hybrid poplar following interactions with Melampsora rust fungi. Mol Plant Microbe Interact 22(2):190–200CrossRefPubMedGoogle Scholar
  17. 17.
    Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature (Lond) 408:796–815CrossRefGoogle Scholar
  18. 18.
    International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature (Lond) 436:793–800CrossRefGoogle Scholar
  19. 19.
    Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, dePamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi, J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D (2006) The genome of black cottonwood Populus trichocarpa (Torr. & Gray) Science 313:1596–1604CrossRefPubMedGoogle Scholar
  20. 20.
    Wilkins O, Nahal H, Foong J, Provert NJ, Campbell MM (2009) Expansion and diversification of the Populus R2R3-MYB family of transcription factors. Plant Physiol 149:981–993CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95:14863–14868CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Iyer VR, Eisen MB, Ross DT, Schler G, Moore T, Lee JCF, Trent JM, Staudt LM, Hudson J, Boguski MS, Lashkari D, Shalon D, Botstein D, Brown PO (1999) The transcriptional program in the response of human fibroblasts to serum. Science 283:83–87CrossRefPubMedGoogle Scholar
  23. 23.
    Li K (2002) Genome-wide coexpression dynamics: theory and application. Proc Natl Acad Sci U S A 99:16875–16880CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Geisler-Lee J, O’Toole N, Ammar R, Provart NJ, Millar AH, Geisler M (2007) A predicted interactome for Arabidopsis. Plant Physiol 145:317–329CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Clifton R, Lister R, Parker KL, Sappl PG, Elhafez D, Millar AH, Day DA, Whelan J (2005) Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana. Plant Mol Biol 58(2):193–212CrossRefPubMedGoogle Scholar
  26. 26.
    Grönlund A, Bhalerao RP, Karlsson J (2009) Modular gene expression in poplar: a multilayer network approach. New Phytol 181(2):315–322CrossRefPubMedGoogle Scholar
  27. 27.
    Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K (2009) ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res 37:D987–D991CrossRefPubMedGoogle Scholar
  28. 28.
    Manfield IW, Jen CH, Pinney JW, Michalopoulos I, Bradford JR, Gilmartin PM, Westhead DR (2006) Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. Nucleic Acids Res 34:W504–W509CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Gene Ontology Consortium (2008) The Gene Ontology project in 2008. Nucleic Acids Res 36:D440–D444CrossRefGoogle Scholar
  30. 30.
    Steinhauser D, Usadel B, Luedemann A, Thimm O, Kopka J (2004) CSB.DB: a comprehensive systems-biology database. Bioinformatics 20(18):3647–3651CrossRefPubMedGoogle Scholar
  31. 31.
    Childs KL, Hamilton JP, Zhu W, Ly E, Cheung F, Wu H, Rabinowicz PD, Town CD, Robin Buell C, Chan AP (2007) The TIGR Plant Transcript Assemblies database. Nucleic Acids Res 35:D846–D851CrossRefPubMedGoogle Scholar
  32. 32.
    Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J (2003) TIGR Gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19(5):651–652CrossRefPubMedGoogle Scholar
  33. 33.
    Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 36:D1009–D1014CrossRefPubMedGoogle Scholar

Copyright information

© The Japan Wood Research Society 2009

Authors and Affiliations

  • Yoshiyuki Ogata
    • 1
  • Hideyuki Suzuki
    • 1
  • Daisuke Shibata
    • 1
  1. 1.Department of Biotechnology ResearchKazusa DNA Research InstituteChibaJapan

Personalised recommendations