Tree Genetics & Genomes

, Volume 9, Issue 4, pp 1031–1041 | Cite as

Transcriptome characterization and detection of gene expression differences in aspen (Populus tremuloides)

  • Hardeep S. Rai
  • Karen E. Mock
  • Bryce A. Richardson
  • Richard C. Cronn
  • Katherine J. Hayden
  • Jessica W. Wright
  • Brian J. Knaus
  • Paul G. Wolf
Original Paper


Aspen (Populus tremuloides) is a temperate North American tree species with a geographical distribution more extensive than any other tree species on the continent. Because it is economically important for pulp and paper industries and ecologically important for its role as a foundation species in forest ecosystems, the decline of aspen in large portions of its range is of serious concern. The availability and annotation of the black cottonwood (Populus trichocarpa) genome enables a range of high throughput sequencing approaches that can be used to understand rangewide patterns of genetic variation, adaptation, and responses to environmental challenges in other Populus species, including aspen. Gene expression studies are particularly useful for understanding the molecular basis of ecological responses, but are limited by the availability of transcriptome data. We explored the aspen transcriptome through the use of high-throughput sequencing with two main goals: (1) characterization of the expressed portion of the P. tremuloides genome in leaves and (2) assessment of variation in gene expression among genets collected from distinct latitudes but reared in a common garden. We also report a large single nucleotide polymorphism dataset that provides the groundwork for future studies of aspen evolution and ecology, and we identify a set of differentially expressed genes across individuals and population boundaries for the leaf transcriptome of P. tremuloides.


Trembling aspen Quaking aspen RNA-Seq Differential expression SNP (single nucleotide polymorphism) Populus trichocarpa 


  1. Bajgain P, Richardson BA, Price JC, Cronn RC, Udall JA (2011) Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata). BMC Genomics 12:370CrossRefPubMedGoogle Scholar
  2. Bashir A, Bansal V, Bafna V (2010) Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance. BMC Genomics 11:385Google Scholar
  3. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc Series B (Methodological) 57:289–300Google Scholar
  4. Beritognolo I, Harfouche A, Brilli F, Prosperini G, Gaudet M, Brosché M, Salani F, Kuzminsky E, Auvinen P, Paulin L (2011) Comparative study of transcriptional and physiological responses to salinity stress in two contrasting Populus alba L. genotypes. Tree Physiol 31(12):1335–1355CrossRefPubMedGoogle Scholar
  5. Bräutigam A, Mullick T, Schliesky S, Weber APM (2011) Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C(3) and C(4) species. J Exp Bot 62:3093–3102CrossRefPubMedGoogle Scholar
  6. Cervera MT, Storme V, Soto A, Ivens B, Van Montagu M, Rajora OP, Boerjan W (2005) Intraspecific and interspecific genetic and phylogenetic relationships in the genus Populus based on AFLP markers. TAG Theoretical Appl Genet 111(7):1440–1456CrossRefGoogle Scholar
  7. Chen JH, Sun H, Wen J, Yang YP (2010) Molecular phylogeny of Salix L. (Salicaceae) inferred from three chloroplast datasets and its systematic implications. Taxon 59(1):29–37Google Scholar
  8. Chen K, Peng Y, Wang Y, Korpelainen H, Li C (2007) Genetic relationships among poplar species in section Tacamahaca (Populus L.) from western Sichuan, China. Plant Sci 172(2):196–203CrossRefGoogle Scholar
  9. Chong DKX, Yang RC, Yeh FC (1994) Nucleotide divergence between populations of trembling aspen (Populus tremuloides) estimated with RAPDS. Curr Genet 26(4):374–376CrossRefPubMedGoogle Scholar
  10. Cohen D, Bogeat-Triboulot MB, Tisserant E, Balzergue S, Martin-Magniette ML, Lelandais G, Ningre N, Renou JP, Tamby JP, Le Thiec D (2010) Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes. BMC Genomics 11(1):630CrossRefPubMedGoogle Scholar
  11. Cole CT (2005) Allelic and population variation of microsatellite loci in aspen (Populus tremuloides). New Phytol 167:155–164CrossRefPubMedGoogle Scholar
  12. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676CrossRefPubMedGoogle Scholar
  13. Coppe A, Pujolar JM, Maes GE, Larsen PF, Hansen MM, Bernatchez L, Zane L, Bortoluzzi S (2010) Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel. BMC Genomics 11:635CrossRefPubMedGoogle Scholar
  14. Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucl Acids Res 36:e122CrossRefPubMedGoogle Scholar
  15. Di Y, Schafer DW, Cumbie JS, Chang JH (2011) The NBP negative binomial model for assessing differential gene expression from RNA-Seq. Stat Appl Genet Mol Biol 10:art24Google Scholar
  16. Eckenwalder J (1977) North American cottonwoods (Populus, Salicaceae) of sections Abaso and Aigeros. J Arnold Arboret 58:193–208Google Scholar
  17. Eckert AJ, Bower AD, Wegrzyn JL, Pande B, Jermstad KD, Krutovsky KV, Clair JBS, Neale DB (2009) Asssociation genetics of coastal Douglas Fir (Pseudotsuga menziesu var. menziesii, Pinaceae). I. cold-hardiness related traits. Genetics 182(4):1289–1302CrossRefPubMedGoogle Scholar
  18. Ellison CE, Hall C, Kowbel D, Welch J, Brem RB, Glass NL, Taylor JW (2011) Population genomics and local adaptation in wild isolates of a model microbial eukaryote. Proc Nat Acad Sci (USA) 108:2831–2836CrossRefGoogle Scholar
  19. Fang Z, Cui X (2011) Design and validation issues in RNA-seq experiments. Brief Bioinform 12:280–287CrossRefPubMedGoogle Scholar
  20. Fisher RA (1922) On the interpretation of χ2 from contingency tables, and the calculation of P. J Roy Stat Soc 85(1):87–94CrossRefGoogle Scholar
  21. Fladung M, Buschbom J (2009) Identification of single nucleotide polymorphisms in different Populus species. Trees-Struct Funct 23(6):1199–1212CrossRefGoogle Scholar
  22. Frey BR, Lieffers VJ, Landhausser SM (2004) Predicting landscape patterns of aspen dieback: mechanisms and knowledge gaps. Canad J Forest Res 34(7):1379–1390CrossRefGoogle Scholar
  23. Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao Y, Tam A, Wang S, Friedmann M, Birol I, Jones SJM, Cronk QCB, Douglas CJ (2011) SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour 11:81–92CrossRefPubMedGoogle Scholar
  24. Grisel N, Zoller S, Künzli-Gontarczyk M, Lampart T, Münsterkötter M, Brunner I, Bovet L, Métraux J-P, Sperisen C (2010) Transcriptome responses to aluminum stress in roots of aspen (Populus tremula). BMC Plant Biol 10:15CrossRefGoogle Scholar
  25. Hamanishi ET, Raj S, Wilkins O, Thomas BR, Mansfield SD, Plant AL, Campbell MM (2010) Intraspecific variation in the Populus balsamifera drought transcriptome. Plant Cell Env 33:1742–1755CrossRefGoogle Scholar
  26. Hamzeh M, Dayanandan S (2004) Phylogeny of Populus (Salicaceae) based on nucleotide sequences of chloroplast trnT-trnF region and nuclear rDNA. Amer J Bot 91(9):1398–1408CrossRefGoogle Scholar
  27. Hamzeh M, Périnet P, Dayanandan S (2006) Genetic relationships among species of Populus (Salicaceae) based on nuclear genomic data. J Torrey Bot Soc 133(4):519–527CrossRefGoogle Scholar
  28. Hogg EH, Brandt JP, Michaelian M (2008) Impacts of a regional drought on the productivity, dieback, and biomass of western Canadian aspen forests. Canad J Forest Res 38:1373–1384CrossRefGoogle Scholar
  29. Hogg EH, Hurdle PA (1995) The aspen parkland in western Canada: a dry-climate analogue for the future boreal forest? Water Air Soil Pollut 82(1):391–400CrossRefGoogle Scholar
  30. Isebrands JG, McDonal EP, Kruger E, Hendrey G, Percy K, Pregitzer K, Sober J, Karnosky DF (2001) Growth responses of Populus tremuloides clones to interacting elevated carbon dioxide and tropospheric ozone. Environ Pollut 115:359–371CrossRefGoogle Scholar
  31. Iverson LR, Prasad AM (2002) Potential redistribution of tree species habitat under five climate change scenarios in the eastern US. For Ecol Manag 155:205–222CrossRefGoogle Scholar
  32. Jiang H, Peng S, Zhang S, Li X, Korpelainen H, Li C (2012) Transcriptional profiling analysis in Populus yunnanensis provides insights into molecular mechanisms of sexual differences in salinity tolerance. J Exp Bot 63:3709–3726Google Scholar
  33. Jones JR (1985) Distribution. In: DeByle NV, Winokur RP (eds) Aspen: ecology and management in the western United States. General Technical Report RM-1 19. US Department of Agriculture, Forest Service, Fort Collins, pp 9–10Google Scholar
  34. Kawahara-Miki R, Wada K, Azuma N, Chiba S (2011) Expression profiling without genome sequence information in a non-model species, pandalid shrimp (Pandalus latirostris), by next-generation sequencing. PLoS One 6(10):e26043CrossRefPubMedGoogle Scholar
  35. Kelleher CT, Wilkin J, Zhuang J, Cortés AJ, Quintero ÁLP, Gallagher TF, Bohlmann J, Douglas CJ, Ellis BE, Ritland K (2012) SNP discovery, gene diversity, and linkage disequilibrium in wild populations of Populus tremuloides. Tree Genet Genomes 8:821–829CrossRefGoogle Scholar
  36. Kurz WA, Apps MJ (1999) A 70-year retrospective analysis of carbon fluxes in the Canadian forest sector. Ecol Appl 9(2):526–547CrossRefGoogle Scholar
  37. Langmead B, Trapnell C, Pop M, Salzberg S (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25CrossRefPubMedGoogle Scholar
  38. Larsen PE, Sreedasyam A, Trivedi G, Podila GK, Cseke LJ, Collart FR (2011) Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome. BMC Systems Biol 5:14CrossRefGoogle Scholar
  39. Liu Z, Furnier GR (1993) Comparison of allozyme, RFLP, and RAPD markers for revealing genetic variation within and between trembling aspen and bigtooth aspen. Theoret Appl Genet 87(1):97–105Google Scholar
  40. Lund ST, Furnier GR, Mohn CA (1992) Isozyme variation in quaking aspen in Minnesota. Canad J Forest Res 22(4):521–524CrossRefGoogle Scholar
  41. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509–1517CrossRefPubMedGoogle Scholar
  42. Matzkin LM (2008) The molecular basis of host adaptation in cactophilic Drosophila: molecular evolution of a glutathione S-transferase gene (GstD1) in Drosophila mojavensis. Genetics 178(2):1073–1083CrossRefPubMedGoogle Scholar
  43. Matzkin LM (2012) Population transcriptomics of cactus host shifts in Drosophila mojavensis. Mol Ecol 21:2428–2439Google Scholar
  44. Metzker ML (2009) Sequencing technologies: the next generation. Nature Rev Genet 11(1):31–46CrossRefPubMedGoogle Scholar
  45. Mitton J, Grant M (1996) Genetic variation and the natural history of quaking aspen. Bioscience 46:25–31CrossRefGoogle Scholar
  46. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (New York, NY) 320:1344–1349CrossRefGoogle Scholar
  47. Novaes E, Drost D, Farmerie W, Pappas G, Grattapaglia D, Sederoff R, Kirst M (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9(1):312CrossRefPubMedGoogle Scholar
  48. Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, Assefa SA, He M, Croucher NJ, Pickard DJ (2009) A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella Typhi. PLoS Genetics 5(7):e1000569CrossRefPubMedGoogle Scholar
  49. Qiu Q, Ma T, Hu Q, Liu B, Wu Y, Zhou H, Wang Q, Wang J, Liu J (2011) Genome-scale transcriptome analysis of the desert poplar, Populus euphratica. Tree Physiol 31(4):452–461CrossRefPubMedGoogle Scholar
  50. Quesada T, Li Z, Dervinis C, Li Y, Bocock PN, Tuskan GA, Casella G, Davis JM, Kirst M (2008) Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms. New Phytol 180:408–420CrossRefPubMedGoogle Scholar
  51. Rehfeldt GE, Ferguson DE, Crookston NL (2009) Aspen, climate, and sudden decline in western USA. For Ecol Manag 258:2353–2364CrossRefGoogle Scholar
  52. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140CrossRefPubMedGoogle Scholar
  53. Schier GA (1978) Vegetative propagation of Rocky Mountain aspen. USDA Forest Service General Technical Report INT-44Google Scholar
  54. Severin AJ, Woody JL, Bolon Y-T, Joseph B, Diers BW, Farmer AD, Muehlbauer GJ, Nelson RT, Grant D, Specht JE, Graham MA, Cannon SB, May GD, Vance CP, Shoemaker RC (2010) RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. BMC Plant Biol 10:16CrossRefGoogle Scholar
  55. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313(5793):1596CrossRefPubMedGoogle Scholar
  56. Unneberg P, Strömberg M, Lundeberg J, Jansson S, Sterky F (2005) Analysis of 70,000 EST sequences to study divergence between two closely related Populus species. Tree Genet Genomes 1(3):109–115CrossRefGoogle Scholar
  57. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev Genet 10:57–63CrossRefPubMedGoogle Scholar
  58. Worrall JJ, Egeland L, Eager T, Mask RA, Johnson EW, Kemp PA, Shepperd WD (2008) Rapid mortality of Populus tremuloides in southwestern Colorado, USA. For Ecol Manag 255(3):686–696CrossRefGoogle Scholar
  59. Zenoni S, Ferrarini A, Giacomelli E, Xumerle L, Fasoli M, Malerba G, Bellin D, Pezzotti M, Delledonne M (2010) Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq. Plant Physiol 152(4):1787–1795CrossRefPubMedGoogle Scholar
  60. Zhou S, Campbell TG, Stone EA, Mackay TFC, Anholt RRH (2012) Phenotypic plasticity of the Drosophila transcriptome. PLoS Genetics 8(3):e1002593CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2013

Authors and Affiliations

  • Hardeep S. Rai
    • 1
  • Karen E. Mock
    • 1
  • Bryce A. Richardson
    • 2
  • Richard C. Cronn
    • 3
  • Katherine J. Hayden
    • 4
  • Jessica W. Wright
    • 5
  • Brian J. Knaus
    • 3
  • Paul G. Wolf
    • 6
  1. 1.Ecology Center and Department of Wildland ResourcesUtah State UniversityLoganUSA
  2. 2.Rocky Mountain Research StationUSDA Forest ServiceProvoUSA
  3. 3.Pacific Northwest Research StationUSDA Forest ServiceCorvallisUSA
  4. 4.Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyUSA
  5. 5.Pacific Southwest Research StationUSDA- Forest ServiceDavisUSA
  6. 6.Ecology Center and Department of BiologyUtah State UniversityLoganUSA

Personalised recommendations