High-throughput analysis of transcriptome variation during water deficit in a poplar hybrid: A general overview

Tree Genetics and Genomes

Volumn 10, Issue 1, 2014, Pages 53-66

  Cossu, Rosa Maria ^a   Giordani, Tommaso ^a   Cavallini, Andrea ^a   Natali, Lucia ^a  

^a UNIVERSITY OF PISA   (Italy)

Author keywords

Drought; Illumina sequencing; Populus hybrid; RNA Seq; Transcriptome

Indexed keywords

EID: 84892447334     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-013-0661-5     Document Type: Article

References (66)

1. Abe H, Yamaguchi-Shinozaki K, Urao T, Iwasaki T, Hosokawa D, Shinozaki K (1997) Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid regulated gene expression. Plant Cell 9: 1859-1868.
2. Apel K, Hirt H (2004) Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annu Rev Plant Biol 55: 373-399.
3. Baggerly KA, Deng L, Morris JS, Aldaz CM (2003) Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics 19: 1477-1483.
4. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
5. Boursiac Y, Boudet J, Postaire O, Luu DT, Tournaire-Roux C, Maurel C (2008) Stimulus-induced downregulation of root water transport involves reactive oxygen species-activated cell signalling and plasma membrane intrinsic protein internalization. Plant J 56: 207-218.
6. Boyer JS (2009) Evans Review: Cell wall biosynthesis and the molecular mechanism of plant enlargement. Funct Plant Biol 36: 383-394.
7. Brinker M, Brosché M, Vinocur B, Abo-Ogiala A, Fayyaz P, Janz D, Ottow EA, Cullmann AD, Saborowski J, Kangasjärvi J, Altman A, Polle A (2010) Linking the salt transcriptome with physiological responses of a salt-resistant Populus species as a strategy to identify genes important for stress acclimation. Plant Physiol 154: 1697-1709.
8. Chen C, Farmer AD, Langley RJ, Mudge J, Crow JA, May GD, Huntley J, Smith AG, Retzel EF (2010) Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes. BMC Plant Biol 10: 280.
9. Chen S, Jiang J, Li H, Liu G (2012) The salt-responsive transcriptome of Populus simonii x Populus nigra via DGE. Gene 504: 203-212.
10. Chinnusamy V, Gong Z, Zhu JK (2008) Abscisic acid-mediated epigenetic processes in plant development and stress responses. J Integr Plant Biol 50: 1187-1195.
11. Cohen D, Bogeat-Triboulot MB, Tisserant E, Balzergue S, Martin-Magniette ML, Lelandais G, Ningre N, Renou JP, Tamby JP, Le Thiec D, Hummel I (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: 630.
12. Cossu RM, Buti M, Giordani T, Natali L, Cavallini A (2012) A computational study of the dynamics of LTR retrotransposons in the Populus trichocarpa genome. Tree Genet Genomes 8: 61-75.
13. Cramer GR, Ergul A, Grimplet J, Tillett RL, Tattersall EAR, Bohlman MC, Vincent D, Sonderegger J, Evans J, Osborne C, Quilici D, Schlauch KA, Schooley DA, Cushman JC (2007) Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles. Funct Integr Genomics 7: 111-134.
14. Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K (2011) Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biology 11: 163.
15. Dinneny JR, Long TA, Wang JY, Jung JW, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein J, Benfey PN (2008) Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 320: 942-945.
16. Dixon RA, Steele CL (1999) Flavonoids and isoflavonoids-a gold mine for metabolic engineering. Trends Plant Sci 4: 394-400.
17. Feist AM, Palsson BO (2008) The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 26: 659-667.
18. Goda H, Sasaki E, Akiyama K, Maruyama-Nakashita A, Nakabayashi K, Li W, Ogawa M, Yamauchi Y, Preston J, Aoki K, Kiba T, Takatsuto S, Fujioka S, Asami T, Nakano T, Kato H, Mizuno T, Sakakibara H, Yamaguchi S, Nambara E, Kamiya Y, Takahashi H, Yokota Hirai M, Sakurai T, Shinozaki K, Saito K, Yoshida S, Shimada Y (2008) The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant J 55: 526-542.
19. Good AG, Zaplachinski ST (1994) The effects of drought stress on free amino acid accumulation and protein synthesis in Brassica napus. Physiol Plant 90: 9-14.
20. Gregory BD, Yazaki J, Ecker JR (2008) Utilizing tiling microarrays for whole genome analysis in plants. Plant J 53: 636-644.
21. Hamanishi ET, Campbell MM (2011) Genome-wide responses to drought in forest trees. Forestry 84: 273-283.
22. Hoen PAC, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RHAM, de Menezes RX, Boer JM, van Ommen GJB, den Dunnen JT (2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucl Acids Res 36: e141.
23. Hubbard KE, Nishimura N, Hitomi K, Getzoff ED, Schroeder JI (2010) Early abscisic acid signal transduction mechanisms: newly discovered components and newly emerging questions. Genes Dev 24: 1695-1708.
24. Hummel I, Pantin F, Sulpice R, Piques M, Rolland G, Dauzat M, Christophe A, Pervent M, Bouteillé M, Stitt M, Gibon Y, Muller B (2010) Arabidopsis plants acclimate to water deficit at low cost through changes of carbon usage: an integrated perspective using growth, metabolite, enzyme, and gene expression analysis. Plant Physiol 154: 357-372.
25. 2+ signaling. Annu Rev Plant Biol 61: 561-591.
26. Kreuzwieser J, Hauberg J, Howell KA, Carroll A, Rennenberg H, Harvey Millar A, Whelan J (2009) Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia. Plant Physiol 149: 461-473.
27. Li B, Qin Y, Duan H, Yin W, Xia X (2011) Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica. J Exp Bot 62: 3765-3779.
28. Liu JX, Howell SH (2010) Endoplasmic reticulum protein quality control and its relationship to environmental stress responses in plants. Plant Cell 22: 2930-2942.
29. Lobell DB, Schlenker W, Costa-Roberts J (2011) Climate trends and global crop production since 1980. Science 333: 616-620.
30. Logemann J, Schell J, Willmitzer L (1987) Improved method for the isolation of RNA from plant tissues. Anal Biochem 163: 16-20.
31. Maestrini P, Cavallini A, Rizzo M, Giordani T, Bernardi R, Durante M, Natali L (2009) Isolation and expression analysis of low temperature-induced genes in white poplar (Populus alba). J Plant Physiol 166: 1544-1556.
32. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
33. Matsui A, Ishida J, Morosawa T, Mochizuki Y, Kaminuma E, Endo TA, Okamoto M, Nambara E, Nakajima M, Kawashima M, Satou M, Kim JM, Kobayashi N, Toyoda T, Shinozaki K, Seki M (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a timing array. Plant Cell Physiol 49: 1135-1149.
34. Matters GL, Scandalios JG (1986) Changes in plant gene expression during stress. Dev Genet 7: 167-175.
35. Mittler R, Vanderauwera S, Suzuki N, Miller G, Tognetti VB, Vandepoele K, Gollery M, Shulaev V, van Breusegem F (2011) ROS signaling: the new wave? Trends Plant Sci 16: 300-309.
36. Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 18: 610-621.
37. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
38. Nanjo T, Futamura N, Nishiguchi M, Igasaki T, Shinozaki K, Shinohara K (2004) Characterization of full-length enriched expressed sequence tags of stress treated poplar leaves. Plant Cell Physiol 45: 1738-1748.
39. Pandey V, Nutter RC, Prediger E (2008) Applied biosystems SOLiD™ system: ligation-based sequencing. In: Jantz M (ed) Next generation genome sequencing: towards personalized medicine. Wiley, Milton, pp 29-41.
40. Peng S, Jiang H, Zhang S, Chen L, Li X, Korpelainen H (2012) Transcriptional profiling reveals sexual differences of the leaf transcriptomes in response to drought stress in Populus yunnanensis. Tree Physiol 32: 1541-1555.
41. Pinheiro C, Chaves MM (2011) Photosynthesis and drought: can we make metabolic connections from available data? J Exp Bot 62: 869-882.
42. 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: 452-461.
43. Raj S, Brautigam K, Hamanishi ET, Wilkins O, Thomas BR, Schroeder W, Mansfield SD, Plant AL, Campbell MM (2011) Clone history shapes Populus drought responses. Proc Natl Acad Sci U S A 108: 12521-12526.
44. Sakamoto H, Maruyama K, Sakuma Y, Meshi T, Iwabuchi M, Shinozaki K, Yamaguchi-Shinozaki K (2004) Arabidopsis Cys2/His2-Type zinc-finger proteins function as transcription repressors under drought, cold, and high-salinity stress conditions. Plant Physiol 136: 2734-2746.
45. Schmidt A, Schmid MW, Grossniklaus U (2012) Analysis of plant germline development by high-throughput RNA profiling: technical advances and new insights. The Plant J 70: 18-29.
46. Shendure J (2008) The beginning of the end for microarrays? Nat Methods 5: 585-587.
47. Skirycz A, Inzé D (2010) More from less: plant growth under limited water. Curr Opin Biotechnol 21: 197-203.
48. Tattersall EA, Grimplet J, Deluc L, Wheatley MD, Vincent D, Osborne C, Ergul A, Lomen E, Blank RR, Schlauch KA, Cushman JC, Cramer GR (2007) Transcript abundance profiles reveal larger and more complex responses of grapevine to chilling compared to osmotic and salinity stress. Funct Integr Genomics 7: 317-333.
49. Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37: 914-939.
50. Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.
51. Uppalapati SR, Marek SM, Lee HK, Nakashima J, Tang J, Sledge MK, Dixon RA, Mysore KS (2009) Global gene expression profiling during Medicago truncatula-Phymatotrichopsis omnivore interaction reveals a role for jasmonic acid, ethylene, and the flavanoid pathway in disease development. Mol Plant-Microbe Inter 22: 7-17.
52. Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M (2009) A guide to using MAPMAN to visualize and compare omics data in plants: a case study in the crop species, Maize. Plant Cell Environ 9: 1211-1229.
53. Wang Z, Zhu Y, Wang L, Liu X, Liu Y, Phillips J, Deng X (2009) A WRKY transcription factor participates in dehydration tolerance in Boea hygrometrica by binding to the W-box elements of the galactinol synthase (BhGolS) promoter. Planta 230: 1155-1166.
54. Wang QQ, Liu F, Chen XS, Ma XJ, Zeng HQ, Yang ZM (2010) Transcriptome profiling of early developing cotton fiber by deep-sequencing reveals significantly differential expression of genes in a fuzzless/lintless mutant. Genomics 96: 369-376.
55. Wilkins O, Waldron L, Nahal H, Provart NJ, Campbell MM (2009) Genotype and time of day shape the Populus drought response. Plant J 60: 703-715.
56. Wilkinson S, Davies WJ (2010) Drought, ozone, ABA and ethylene: new insights from cell to plant to community. Plant Cell Environ 33: 510-525.
57. Wu T, Qin ZW, Zhou XY, Feng Z, Du YL (2010) Transcriptome profile analysis of floral sex determination in cucumber. J Plant Physiol 167: 905-913.
58. Xiang Y, Tang N, Du H, Ye H, Xiong L (2008) Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiol 148: 1938-1952.
59. Yamaguchi-Shinozaki K, Shinozaki K (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol 57: 781-803.
60. Yan DH, Fenning T, Tang S, Xia X, Yin W (2012) Genome-wide transcriptional response of Populus euphratica to long-term drought stress. Plant Sci 195: 24-35.
61. Yang SS, Tu ZJ, Cheung F, Xu WW, Lamb JAFS, Jung HJG, Vance CP, Gronwald JW (2011a) Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 12: 199.
62. Yang X, Tschaplinski TJ, Hurst GB, Jawdy S et al (2011b) Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Res 21: 634-641.
63. Yoo SD, Cho Y, Sheen J (2009) Emerging connections in the ethylene signaling network. Trends Plant Sci 14: 270-279.
64. Zeller G, Henz SR, Widmer CK, Sachsenberg T, Rtsch G, Weigel D, Laubinger S (2009) Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. Plant J 58: 1068-1082.
65. 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: 1787-1795.
66. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SWL, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189-1201.