Abstract
Freezing tolerance in plants is obtained during a period of low non-freezing temperatures before the winter sets on, through a biological process known as cold acclimation. Cold is one of the major stress factors that limits the growth, productivity and distribution of plants, and understanding the mechanism of cold tolerance is therefore important for crop improvement. Expressed sequence tags (EST) analysis is a powerful, economical and time-efficient way of assembling information on the transcriptome. To date, several EST sets have been generated from cold-induced cDNA libraries from several different plant species. In this study we utilize the variation in the frequency of ESTs sampled from different cold-stressed plant libraries, in order to identify genes preferentially expressed in cold in comparison to a number of control sets. The species included in the comparative study are oat (Avena sativa), barley (Hordeum vulgare), wheat (Triticum aestivum), rice (Oryza sativa) and Arabidopsis thaliana. However, in order to get comparable gene expression estimates across multiple species and data sets, we choose to compare the expression of tentative ortholog groups (TOGs) instead of single genes, as in the normal procedure. We consider TOGs as preferentially expressed if they are detected as differentially expressed by a test statistic and up-regulated in comparison to all control sets, and/or uniquely expressed during cold stress, i.e., not present in any of the control sets. The result of this analysis revealed a diverse representation of genes in the different species. In addition, the derived TOGs mainly represent genes that are long-term highly or moderately expressed in response to cold and/or other stresses.
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References
Browse, J., Xin, Z.: Temperature sensing and cold acclimation. Current Opinion in Plant Biology 4, 241–246 (2001)
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. 29(6), 693–704 (2002)
Sharma, P., Sharma, N., Deswal, R.: The molecular biology of the low-temperature response in plants. BioEssays 27, 1048–1059 (2005)
Smallwood, M., Bowles, D.J.: Plants in cold climate. The Royal Society 357, 831–847 (2002)
Stitt, M., Hurry, V.: A plant for all seasons: alterations in photosynthetic carbon metabolism during cold acclimation in Arabidopsis. Current Opinion in Plant Biology 5, 199–206 (2002)
Thomashow, M.F.: Plant Cold Acclimation: Freezing Tolerance Genes and Regulatory Mechanisms. Annual Reviews in Plant Physiology and Plant Molecular Biology 50, 571–599 (1999)
Venter, J.C., et al.: Massive parallelism, randomness and genomic advances. Nature Genetics 33, 219–227 (2003)
Lindlof, A.: Gene identification through large-scale EST sequencing processing. Applied Bioinformatics 2, 123–129 (2003)
Mayer, K., Mewes, H.W.: How can we deliver the large plant genomes? Strategies and perspectives. Current Opinion in Plant Biology 5, 173–177 (2002)
Rudd, S.: Expressed sequence tags: alternative or complement to whole genome sequences? Trends in Plant Science 8, 321–329 (2003)
Fei, Z., et al.: Comprehensive EST analysis of tomato and comparative genomics of fruit ripening. The Plant Journal 40, 47–59 (2004)
Romualdi, C., Bortoluzzi, S., Danieli, G.A.: Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests. Human Molecular Genetics 10, 2133–2141 (2001)
Wu, X.-L., et al.: Census of orthologous genes and self-organizing maps of biologically relevant transcriptional patterns in chickens (Gallus gallus). Gene 340, 213–225 (2004)
Audic, S., Claverie, J.-M.: The Significance of Digital Gene Expression Profiles. Genome Research 7, 986–995 (1997)
Claverie, J.-M.: Computational methods for the identification of differential and coordinated gene expression. Human Molecular Genetics 8, 1821–1832 (1999)
Jung, S.H., Lee, J.Y., Lee, D.H.: Use of sage technology to reveal changes in gene expression in arabidopsis leaves undergoing cold stress. Plant Molecular Biology 52, 553–567 (2003)
Schmitt, A.O., et al.: Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissue. Nucleic Acids Research 27, 4251–4260 (1999)
Stekel, D.J., Git, Y., Falciani, F.: The Comparison of Gene Expression from Multiple cDNA libraries. Genome Research 10, 2055–2061 (2000)
Strausberg, R.L., et al.: In Silico analysis of cancer through the Cancer Genome Anatomy Project. TRENDS in Cell Biology 11, S66–S70 (2001)
Lee, Y., et al.: Cross-referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Research 12, 493–502 (2002)
Li, L., Stoeckert, J.C.J., Roos, D.S.: OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Research 13, 2178–2189 (2003)
Bräutigam, M., et al.: Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa. BMC Plant Biology 5, 18 (2005)
Parkinson, J., Guiliano, D.B., Blaxter, M.: Making sense of EST sequences by CLOBBing them. BMC Bioinformatics 3, 31 (2002)
Huang, X., Madan, A.: CAP3: A DNA sequence assembly program. Genome Research 9, 868–877 (1999)
Quackenbush, J., et al.: The TIGR Gene Indices: reconstruction and representation of expressed genes. Nucleic Acids Research 28, 141–145 (2000)
Zhang, J.Z., Creelman, R.A., Zhu, J.-K.: From Laboratory to Field. Using information from Arabidopsis to Engineer Salt, Cold and Drought Tolerance in Crops. Plant Physiology 135, 615–624 (2004)
Chen, W., et al.: Expression profile matrix of arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell 14, 559–574 (2002)
Fowler, S., Thomashow, M.F.: Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the cbf cold response pathway. Plant Cell 14, 1675–1690 (2002)
Kreps, J.A., et al.: Transcriptome changes for arabidopsis in response to salt, osmotic, and cold stress. Plant Physiology 130, 2129–2141 (2002)
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 31, 279–292 (2002)
Vogel, J.T., et al.: Roles of the cbf2 and zat12 transcription factors in configuring the low temperature transcriptome of arabidopsis. Plant Journal 41, 195–211 (2005)
Hannah, M.A., Heyer, A.G., Hincha, D.K., Global, A.: Survey of Gene Regulation during Cold Acclimation in Arabidopsis thaliana. PLoS Genetics 1, e26 (2005)
Li, Q.-B., Haskell, D.W., Guy, C.L.: 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 39, 21–34 (1999)
Danyluk, J., et al.: Differential expression of a gene encoding an acidic dehydrin in chilling sensitive and freezing tolerant gramineae species. FEBS Letter 344, 20–24 (1994)
Christie, P.J., Hahn, M., Walbot, V.: Low-temperature accumulation of alcohol dehydrogenase-1 mRNA and protein activity in maize and rice seedlings. Plant Physiology 95, 699–706 (1991)
Jarillo, J.A., et al.: Low temperature Induces the Accumulation of Alcohol Dehydrogenase mRNA in Arabidosis thaliana, a Chilling-Tolerant Plant. Plant Physiology 101, 833–837 (1993)
Jeong, M.J., Park, S.C., Byun, M.O.: Improvement of salt tolerance in transgenic potato plants by glyceraldehyde-3 phosphate dehydrogenase gene transfer. Mol. Cells 12(2), 185–189 (2001)
Seppanen, M.M., et al.: Characterization and expression of cold-induced glutathione S-transferase in freezing tolerant Solanum commersonii, sensitive S. Plant Science 153(2), 125–133 (2000)
Yang, D.H., Paulsen, H., Andersson, B.: The N-terminal domain of the light-harvesting chlorophyll a/b-binding protein complex (LHCII) is essential for its acclimative proteolysis. FEBS Lett. 466(2-3), 385–388 (2000)
Toyama, T., Teramoto, H., Takeba, G.: 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. 37(7), 1038–1041 (1996)
Gulick, P.J., et al.: Transcriptome comparison of winter and spring wheat responding to low temperature. Genome 48(5), 913–923 (2005)
Bosl, A., Bock, A.: Ribosomal mutation in Escherichia coli affecting membrane stability. Mol. Gen. Genet. 182(2), 358–360 (1981)
Chinnusamy, V., et al.: Ice1: A regulator of cold-induced transcriptome and freezing tolerance in arabidopsis. Genes & Development 17, 1043–1054 (2003)
Wu, K.L., et al.: The WRKY family of transcription factors in rice and Arabidopsis and their origins. DNA Res 12(1), 9–26 (2005)
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, 1–10 (2006)
Thomashow, M.F.: So What’s new in the field of plant cold acclimation? Lots! Plant Physiology 125, 89–93 (2001)
Skinner, J.S., et al.: Structural, functional and phylogenetic characterization of a large CBF gene family in barley. Plant Molecular Biology 59, 533–551 (2005)
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Lindlöf, A., Bräutigam, M., Chawade, A., Olsson, B., Olsson, O. (2007). Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis Through Comparative Analysis of Multiple EST Sets. In: Hochreiter, S., Wagner, R. (eds) Bioinformatics Research and Development. BIRD 2007. Lecture Notes in Computer Science(), vol 4414. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71233-6_5
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DOI: https://doi.org/10.1007/978-3-540-71233-6_5
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