Identification of cold-induced genes in cereal crops and arabidopsis through comparative analysis of multiple EST sets

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4414 LNBI, Issue , 2007, Pages 48-65

  Lindlöf, Angelica ^a   Bräutigam, Marcus ^b   Chawade, Aakash ^b   Olsson, Björn ^a   Olsson, Olof ^b  

^a UNIVERSITY OF SKÖVDE   (Sweden)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FREEZING; IDENTIFICATION (CONTROL SYSTEMS); PLANTS (BOTANY); STRESS ANALYSIS;

ARABIDOPSIS; BIOLOGICAL PROCESS; COMPARATIVE ANALYSIS; FREEZING TOLERANCE; MULTIPLE EST SETS;

GENE EXPRESSION;

EID: 34548078765     PISSN: 03029743     EISSN: 16113349     Source Type: Conference Proceeding    
DOI: 10.1007/978-3-540-71233-6_5     Document Type: Conference Paper

References (47)

1. Browse, J. and Z. Xin, Temperature sensing and cold acclimation. Current Opinion in Plant Biology., 2001. 4: p. 241-246.
2. Kim, H.J., et al., Light signalling mediated by phytochrome plays an important role in cold-induced gene expression through the C-repeat/dehydration responsive element (C/DRE) in Arabidopsis thaliana. Plant J, 2002. 29(6): p. 693-704.
3. Sharma, P., N. Sharma, and R. Deswal, The molecular biology of the low-temperature response in plants. BioEssays, 2005. 27: p. 1048-1059.
4. Smallwood, M. and D.J. Bowles, Plants in cold climate. The Royal Society, 2002. 357: p. 831-847.
5. Stitt, M. and V. Hurry, A plant for all seasons: alterations in photosynthetic carbon metabolism during cold acclimation in Arabidopsis. Current Opinion in Plant Biology, 2002. 5: p. 199-206.
6. Thomashow, M.F., Plant Cold Acclimation: Freezing Tolerance Genes and Regulatory Mechanisms. Annual Reviews in Plant Physiology and Plant Molecular Biology., 1999. 50: p. 571-599.
7. Venter, J.C., et al., Massive parallelism, randomness and genomic advances. Nature Genetics, 2003. 33: p. 219-227.
8. Lindlof, A., Gene identification through large-scale EST sequencing processing. Applied Bioinformatics, 2003. 2: p. 123-129.
9. Mayer, K. and H.W. Mewes, How can we deliver the large plant genomes? Strategies and perspectives. Current Opinion in Plant Biology, 2002. 5: p. 173-177.
10. Rudd, S., Expressed sequence tags: alternative or complement to whole genome sequences? Trends in Plant Science, 2003. 8: p. 321-329.
11. Fei, Z., et al., Comprehensive EST analysis of tomato and comparative genomics of fruit ripening. The Plant Journal, 2004. 40: p. 47-59.
12. Romualdi, C., S. Bortoluzzi, and G.A. Danieli, Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests. Human Molecular Genetics, 2001.10: p. 2133-2141.
13. Wu, X.-L., et al., Census of orthologous genes and self-organizing maps of biologically relevant transcriptional patterns in chickens (Gallus gallus). Gene, 2004. 340: p. 213-225.
14. Audic, S. and J.-M. Claverie, The Significance of Digital Gene Expression Profiles. Genome Research, 1997. 7: p. 986-995.
15. Claverie, J.-M., Computational methods for the identification of differential and coordinated gene expression. Human Molecular Genetics, 1999. 8: p. 1821-1832.
16. Jung, S.H., J.Y. Lee, and D.H. Lee, Use of sage technology to reveal changes in gene expression in arabidopsis leaves undergoing cold stress. Plant Molecular Biology, 2003. 52: p. 553-567.
17. Schmitt, A.O., et al., Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissue. Nucleic Acids Research, 1999. 27: p. 4251-4260.
18. Stekel, D.J., Y. Git, and F. Falciani, The Comparison of Gene Expression from Multiple cDNA libraries. Genome Research, 2000. 10: p. 2055-2061.
19. Strausberg, R.L., et al., In Silico analysis of cancer through the Cancer Genome Anatomy Project. TRENDS in Cell Biology, 2001. 11: p. S66-S70.
20. Lee, Y., et al., Cross-referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Research, 2002. 12: p. 493-502.
21. Li, L., J.C.J. Stoeckert, and D.S. Roos, OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Research, 2003.13: p. 2178-2189.
22. Bräutigam, M., et al., Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa. BMC Plant Biology, 2005. 5: p. 18.
23. Parkinson, J., D.B. Guiliano, and M. Blaxter, Making sense of EST sequences by CLOBBing them. BMC Bioinformatics, 2002. 3: p. 31.
24. Huang, X. and A. Madan, CAP3: A DNA sequence assembly program. Genome Research, 1999. 9: p. 868-877.
25. Quackenbush, J., et al., The TIGR Gene Indices: reconstruction and representation of expressed genes. Nucleic Acids Research, 2000. 28: p. 141-145.
26. Zhang, J.Z., R.A. Creelman, and J.-K. Zhu, From Laboratory to Field. Using information from Arabidopsis to Engineer Salt, Cold and Drought Tolerance in Crops. Plant Physiology, 2004. 135: p. 615-624.
27. Chen, W., et al., Expression profile matrix of arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell, 2002. 14: p. 559-574.
28. Fowler, S. and M.F. Thomashow, Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the cbf cold response pathway.. Plant Cell, 2002. 14: p. 1675-1690.
29. Kreps, J.A., et al., Transcriptome changes for arabidopsis in response to salt, osmotic, and cold stress. Plant Physiology, 2002. 130: p. 2129-2141.
30. Seki, M., et al., Monitoring the expression profiles of 7000 arabidopsis genes under drought, cold and high-salinity stresses using a full-length cdna microarray. Plant Journal, 2002. 31: p. 279-292.
31. Vogel, J.T., et al., Roles of the cbf2 and zat12 transcription factors in configuring the low temperature transcriptome of arabidopsis. Plant Journal, 2005. 41: p. 195-211.
32. Hannah, M.A., A.G. Heyer, and D.K. Hincha, A Global Survey of Gene Regulation during Cold Acclimation in Arabidopsis thaliana. PLoS Genetics, 2005. 1: p. e26.
33. Li, Q.-B., D.W. Haskell, and C.L. Guy, Coordinate and non-coordinate expression of the stress 70 family and other molecular chaperones at high and low temperature in spinach and tomato. Plant Molecular Biology, 1999. 39: p. 21-34.
34. Danyluk, J., et al., Differential expression of a gene encoding an acidic dehydrin in chilling sensitive and freezing tolerant gramineae species. FEBS Letter, 1994. 344: p. 20-24.
35. Christie, P.J., M. Hahn, and V. Walbot, Low-temperature accumulation of alcohol dehydrogenase-1 mRNA and protein activity in maize and rice seedlings. Plant Physiology, 1991. 95: p. 699-706.
36. Jarillo, J.A., et al., Low temperature Induces the Accumulation of Alcohol Dehydrogenase mRNA in Arabidosis thaliana, a Chilling-Tolerant Plant. Plant Physiology, 1993. 101: p. 833-837.
37. Jeong, M.J., S.C. Park, and M.O. Byun, Improvement of salt tolerance in transgenic potato plants by glyceraldehyde-3 phosphate dehydrogenase gene transfer. Mol Cells, 2001. 12(2): p. 185-9.
38. Seppanen, M.M., et al., Characterization and expression of cold-induced glutathione S-transferase in freezing tolerant Solanum commersonii, sensitive S. tuberosum and their interspecific somatic hybrids. Plant Science, 2000. 153(2): p. 125-133.
39. Yang, D.H., H. Paulsen, and B. Andersson, The N-terminal domain of the light-harvesting chlorophyll a/b-binding protein complex (LHCII) is essential for its acclimative proteolysis. FEBS Lett, 2000. 466(2-3): p. 385-8.
40. Toyama, T., H. Teramoto, and G. Takeba, The level of mRNA transcribed from psaL, which encodes a subunit of photosystem I, is increased by cytokinin in darkness in etiolated cotyledons of cucumber. Plant Cell Physiol, 1996. 37(7): p. 1038-41.
41. Gulick, P.J., et al., Transcriptome comparison of winter and spring wheat responding to low temperature. Genome, 2005. 48(5): p. 913-23.
42. Bosl, A. and A. Bock, Ribosomal mutation in Escherichia coli affecting membrane stability. Mol Gen Genet, 1981. 182(2): p. 358-60.
43. Chinnusamy, V., et al., Ice1: A regulator of cold-induced transcriptome and freezing tolerance in arabidopsis. Genes & Development, 2003. 17: p. 1043-1054.
44. Wu, K.L., et al., The WRKY family of transcription factors in rice and Arabidopsis and their origins. DNA Res, 2005. 12(1): p. 9-26.
45. Shinozuka, H., et al., Gene expression and genetic mapping analyses of a perennial ryegrass glycine-rich RNA-binding protein gene suggest a role in cold adaptation. Mol Genet Genomics, 2006: p. 1-10.
46. Thomashow, M.F., So What's new in the field of plant cold acclimation? Lots! Plant Physiology, 2001. 125: p. 89-93.
47. Skinner, J.S., et al., Structural, functional and phylogenetic characterization of a large CBF gene family in barley. Plant Molecular Biology, 2005. 59: p. 533-551.