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The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE

By Carlos Molina, Mainassara Zaman-Allah, Faheema Khan, Nadia Fatnassi, Ralf Horres, Björn Rotter, Diana Steinhauer, Laurie Amenc, Jean-Jacques Drevon, Peter Winter and Günter Kahl
Topics: Research Article
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:3045889
Provided by: PubMed Central

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  1. (2011). A new mathematical model for relative quantification in realtime RT-PCR. Nucleic Acids Res 2001, 29:e45. doi:10.1186/1471-2229-11-31 Cite this article as: Molina et al.: The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE.
  2. A: Ectomycorrhiza and hydrogel protect hybrid poplar from water deficit and unravel plastic responses of xylem anatomy.
  3. (2004). A: SOS3 (salt overly sensitive 3) from Arabidopsis thaliana: expression, purification, crystallization and preliminary X-ray analysis. Acta Crystallog D
  4. (2004). Abdelly C: Effect of salinity on root-nodule conductance to the oxygen diffusion in the Medicago truncatulaSinorhizobium meliloti symbiosis. Plant Physiol Biochem
  5. (2003). Akil H: Evaluation of Sensitivity, Performance and Reproducibility
  6. (2009). al: A comprehensive resource of droughtand salinity-responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics
  7. (2003). al: Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol
  8. (2006). Alfalfa Mob1-like proteins are involved in cell proliferation and are localized in the cell division plane during cytokinesis. Exp Cell Res
  9. (2005). Applications of DNA microarrays in biology. Annu Rev Biochem
  10. (2004). BD: Mitochondrial complex I mutations in Caenorhabditis elegans produce cytochrome c oxidase deficiency, oxidative stress and vitamin-responsive lactic acidosis. Human Mol Gen
  11. (2000). Breusegem F: Dual action of the active oxygen species during plant stress responses. Cell Mol Life Sci
  12. (2006). Breusegem F: Transcriptomic footprints disclose specificity of reactive oxygen species signaling in Arabidopsis. Plant Physiol
  13. (2006). Chickpea molecular breeding: New tools and concepts. Euphytica
  14. (2004). CW: Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. Mol Cell
  15. (2001). Cysteine Synthase Overexpression in Tobacco Confers Tolerance to Sulfur-Containing Environmental Pollutants. Plant Physiol
  16. (2004). De Souza SJ, Camargo AA: The impact of SNPs on the interpretation of SAGE and MPSS experimental data. Nucl Acids Res
  17. (2007). DH: The promoters of Arabidopsis thaliana genes AtCOX17-1 and -2, encoding a copper chaperone involved in cytochrome c oxidase biogenesis, are preferentially active in roots and anthers and induced by biotic and abiotic stress. Physiol Plantarum
  18. (2001). DW: Molecular cloning: a laboratory manual. 3 edition.
  19. (2007). Effect of salinity on root-nodule conductance to the oxygen diffusion in the Cicer arietinumMesorhizobium ciceri symbiosis.
  20. (2005). ErmineJ: tool for functional analysis of gene expression data sets.
  21. (2005). et al: High-throughput SNP genotyping on universal bead arrays. Mutat Res
  22. (2004). et al: The Arabidopsis root transcriptome by serial analysis of gene expression. Gene identification using the genome sequence. Plant Physiol
  23. (2005). et al: Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science
  24. (1994). Extensin gene expression is induced by mechanical stimuli leading to local cell wall strengthening in Nicotiana plumbaginifolia. Planta
  25. (2006). Feldmann K: Features of Arabidopsis Genes and Genome Discovered using Fulllength cDNAs. Plant Molecular Biology
  26. (2007). Fernandes de Melo D: Alternative oxidase regulation in roots of Vigna unguiculata cultivars differing in drought/ salt tolerance.
  27. Gene function analysis in complex data sets using ErmineJ. Nat Protoc 5:1148-1159.
  28. (2007). Genome-Wide Analysis of mRNA Decay Rates and Their Determinants in Arabidopsis thaliana. Plant Cell
  29. (2005). Gingeras TR: Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res
  30. (2002). GJ: An anatomy of normal and malignant gene expression. Proc Natl Acad Sci USA
  31. (2002). Golldack D: Salt-induced expression of NADP-dependent isocitrate dehydrogenase and ferredoxin-dependent glutamate synthase in Mesembryanthemum crystallinum. Planta
  32. (2007). Guo Y: SCABP8/CBL10, a Putative Calcium Sensor, Interacts with the Protein Kinase SOS2 to Protect Arabidopsis Shoots from Salt Stress. Plant Cell
  33. (2004). Hirt H: Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annu Rev Plant Biol
  34. (2001). HJ: Gene expression profiles during the initial phase of salt stress in rice. Plant Cell
  35. (2005). HJ: The maize root transcriptome by serial analysis of gene expression. Plant Physiol
  36. (2001). Hyperosmotic stress induces the rapid phosphorylation of a soybean phosphatidylinositol transfer protein homolog through activation of the protein kinases SPK1 and SPK2. Plant Cell
  37. (2001). Izui K: A Ca(2+)-dependent protein kinase that endows rice plants with cold- and salt-stress tolerance functions in vascular bundles. Plant Cell Physiol
  38. (2002). JB: Reactive oxygen species, antioxidant systems and nitric oxide in peroxisomes.
  39. (2001). JD: Calcium-dependent protein kinases play an essential role in a plant defence response.
  40. (2007). JK: SOS2 promotes salt tolerance in part by interacting with the vacuolar H+-ATPase and upregulating its transport activity. Mol Cell Biol
  41. (2004). KD: The protein kinase SOS2 activates the Arabidopsis H(+)/Ca(2+) antiporter CAX1 to integrate calcium transport and salt tolerance.
  42. (2006). Laloi C: Reactive oxygen species as signals that modulate plant stress responses and programmed cell death. Bioessays
  43. (1994). Lamport DT: Extensin: repetitive motifs, functional sites, post-translational codes, and phylogeny.
  44. (2005). Lauriere C: Osmotic signaling in plants: multiple pathways mediated by emerging kinase families. Plant Physiol
  45. (1990). Lipman DJ: Basic local alignment search tool.
  46. (2001). Lluch C: Effects of salinity on protein and lipopolysaccharide pattern in a salt-tolerant strain of Mesorhizobium ciceri.
  47. (2004). Localization of superoxide dismutases and hydrogen peroxide in legume root nodules. Mol Plant Microbe Interact
  48. (2001). Managing water for people and nature. Science
  49. (2005). MAPK signalling and plant cell survival in response to oxidative environmental stress. Plant Responses to Air Pollution and Global Change
  50. (2005). Murooka Y: Expression of
  51. (2000). Nishimura A: Effects of aldehyde dehydrogenase and acetyl-CoA synthetase on acetate formation in sake mash.
  52. (2003). Noctor G: Redox sensing and signalling associated with reactive oxygen in chloroplasts, peroxisomes and mitochondria. Physiol Plantarum
  53. (2007). Origin of phenotypes: Genes and transcripts. Genome Res
  54. (2008). Oxylipin signaling in plant stress responses. Plant Cell
  55. (2007). Pang EC: Transcriptional profiling of chickpea genes differentially regulated in response to high-salinity, cold and drought.
  56. (2000). Plant cellular and molecular responses to high salinity. Annu Rev Plant Physiol Plant Mol Biol
  57. (2001). Plant mitochondria and oxidative stress: Electron Transport, NADPH Turnover, and Metabolism of Reactive Oxygen Species. Annu Rev Plant Physiol Plant Mol Biol
  58. (1982). Plant Productivity and Environment.
  59. (2001). PM: Genes that are uniquely stress regulated in salt overly sensitive (sos) mutants. Plant Physiol
  60. (2009). Polle A: Upgrading root physiology for stress tolerance by ectomycorrhizas: insights from metabolite and transcriptional profiling into reprogramming for stress anticipation. Plant Physiol
  61. (2000). Reactive oxygen species and antioxidants in legume nodules. Physiol Plantarum
  62. (2006). Reactive oxygen species and reactive nitrogen species in peroxisomes. Production, scavenging, and role in cell signaling. Plant Physiol
  63. (2002). Regulation of SOS1, a plasma membrane
  64. S: Differential impact of lipoxygenase 2 and jasmonates on natural and stress-induced senescence in Arabidopsis.
  65. (2002). Salt and drought stress signal transduction in plants. Annu Rev Plant Biol
  66. (2002). Schilmiller AL: Oxylipin metabolism in response to stress. Curr Opin Plant Biol
  67. (2003). Sekimizu K: Transcription elongation factor S-II maintains transcriptional fidelity and confers oxidative stress resistance. Genes to Cells
  68. (2009). Singla-Pareek SL, Pareek A: Physiological responses among Brassica species under salinity stress show strong correlation with transcript abundance for SOS pathway-related genes.
  69. (2006). SM: Pan-genome isolation of low abundance transcripts using SAGE tag. FEBS Lett
  70. (2005). Soreq H: Function of alternative splicing. Gene
  71. (1996). SS: Differential levels of wheat germ agglutinin (WGA) in germinating embryos of different wheat cultivars in response to osmotic stress. Plant Physiol Biochem
  72. (1999). SS: Enhanced wheat germ agglutinin accumulation in the germinating embryos of wheat (Triticum aestivum L.) appears to be a general stress response. Current Science
  73. (2009). Stintzi A: Enzymes in jasmonate biosynthesis - structure, function, regulation. Phytochemistry
  74. (2007). Structure and functions of plant calciumdependent protein kinases. Acta Biochim Pol
  75. (2006). SuperSAGE array: the direct use of 26-base-pair transcript tags in oligonucleotide arrays. Nat Methods
  76. (2005). SuperSAGE combined with PCR walking allows global gene expression profiling of banana (Musa acuminata), a non-model organism. Theor Appl Genet
  77. (2008). SuperSAGE: the drought stressresponsive transcriptome of chickpea roots.
  78. (2005). SY: AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J
  79. (2007). The adverse effects of soil salinization on the growth of Trifolium alexandrinum L. and associated microbial and biochemical properties in a soil from Iran. Soil Biol and Biochem
  80. (2000). The Arabidopsis thaliana SOS2 gene encodes a protein kinase that is required for salt tolerance. Proceed Nat Acad Sci USA
  81. (2004). The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis. Mol Cell
  82. (2004). The SOS3 family of calcium sensors and SOS2 family of protein kinases in Arabidopsis. Plant Physiol
  83. (2002). Transcript abundance in yeast varies over six orders of magnitude.
  84. (2004). Trypsin and alpha-amylase inhibitors are differentially induced in leaves of amaranth (Amaranthus hypochondriacus) in response to biotic and abiotic stress. Physiol Plantarum
  85. (2008). Tuteja N: Calcium- and salt-stress signaling in plants: shedding light on SOS pathway. Arch Biochem Biophys
  86. (2001). UA: Detection of mitochondrial single nucleotide polymorphisms using a primer elongation reaction on oligonucleotide microarrays. Nucleic Acids Res
  87. (2004). Udvardi MK: Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes.
  88. Zhang HX: The woody plant poplar has a functionally conserved salt overly sensitive pathway in response to salinity stress.