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

Tree Genetics and Genomes

Volumn 9, Issue 4, 2013, Pages 1031-1041

  Rai, Hardeep S ^a   Mock, Karen E ^a   Richardson, Bryce A ^b   Cronn, Richard C ^c   Hayden, Katherine J ^d   Wright, Jessica W ^e   Knaus, Brian J ^c   Wolf, Paul G ^a  

^a UTAH STATE UNIVERSITY   (United States)

^b USDA FOREST SERVICE   (United States)

^c PACIFIC NORTHWEST RESEARCH STATION   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e PACIFIC SOUTHWEST RESEARCH STATION   (United States)

Author keywords

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

Indexed keywords

POPULUS; POPULUS TREMULOIDES; POPULUS TRICHOCARPA;

EID: 84880159332     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-013-0615-y     Document Type: Article

References (60)

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: 370.
2. Bashir A, Bansal V, Bafna V (2010) Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance. BMC Genomics 11: 385.
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: 289-300.
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): 1335-1355.
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: 3093-3102.
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): 1440-1456.
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): 29-37.
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): 196-203.
9. Chong DKX, Yang RC, Yeh FC (1994) Nucleotide divergence between populations of trembling aspen (Populus tremuloides) estimated with RAPDS. Curr Genet 26(4): 374-376.
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): 630.
11. Cole CT (2005) Allelic and population variation of microsatellite loci in aspen (Populus tremuloides). New Phytol 167: 155-164.
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): 3674-3676.
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: 635.
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: e122.
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: art24.
16. Eckenwalder J (1977) North American cottonwoods (Populus, Salicaceae) of sections Abaso and Aigeros. J Arnold Arboret 58: 193-208.
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): 1289-1302.
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: 2831-2836.
19. Fang Z, Cui X (2011) Design and validation issues in RNA-seq experiments. Brief Bioinform 12: 280-287.
20. 2 from contingency tables, and the calculation of P. J Roy Stat Soc 85(1): 87-94.
21. Fladung M, Buschbom J (2009) Identification of single nucleotide polymorphisms in different Populus species. Trees-Struct Funct 23(6): 1199-1212.
22. Frey BR, Lieffers VJ, Landhausser SM (2004) Predicting landscape patterns of aspen dieback: mechanisms and knowledge gaps. Canad J Forest Res 34(7): 1379-1390.
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: 81-92.
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: 15.
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: 1742-1755.
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): 1398-1408.
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): 519-527.
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: 1373-1384.
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): 391-400.
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: 359-371.
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: 205-222.
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: 3709-3726.
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 9-10.
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): e26043.
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: 821-829.
36. Kurz WA, Apps MJ (1999) A 70-year retrospective analysis of carbon fluxes in the Canadian forest sector. Ecol Appl 9(2): 526-547.
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): R25.
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: 14.
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): 97-105.
40. Lund ST, Furnier GR, Mohn CA (1992) Isozyme variation in quaking aspen in Minnesota. Canad J Forest Res 22(4): 521-524.
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: 1509-1517.
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): 1073-1083.
43. Matzkin LM (2012) Population transcriptomics of cactus host shifts in Drosophila mojavensis. Mol Ecol 21: 2428-2439.
44. Metzker ML (2009) Sequencing technologies: the next generation. Nature Rev Genet 11(1): 31-46.
45. Mitton J, Grant M (1996) Genetic variation and the natural history of quaking aspen. Bioscience 46: 25-31.
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: 1344-1349.
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): 312.
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): e1000569.
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): 452-461.
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: 408-420.
51. Rehfeldt GE, Ferguson DE, Crookston NL (2009) Aspen, climate, and sudden decline in western USA. For Ecol Manag 258: 2353-2364.
52. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
53. Schier GA (1978) Vegetative propagation of Rocky Mountain aspen. USDA Forest Service General Technical Report INT-44.
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: 16.
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): 1596.
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): 109-115.
57. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev Genet 10: 57-63.
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): 686-696.
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): 1787-1795.
60. Zhou S, Campbell TG, Stone EA, Mackay TFC, Anholt RRH (2012) Phenotypic plasticity of the Drosophila transcriptome. PLoS Genetics 8(3): e1002593.