Plant Physiology Preview
Published on September 16, 2005; 10.1104/pp.105.066134
Received May 27, 2005
Returned for revision July 20, 2005
Accepted July 26, 2005
Sorghum Expressed Sequence Tags Identify Signature Genes for Drought, Pathogenesis, and Skotomorphogenesis from a Milestone Set of 16,801 Unique Transcripts
Lee H. Pratt *, Chun Liang , Manish Shah , Feng Sun , Haiming Wang , St. Patrick Reid , Alan R. Gingle , Andrew H. Paterson , Rod Wing , Ralph Dean , Robert Klein , Henry T. Nguyen , Hong-mei Ma , Xin Zhao , Daryl T. Morishige , John E. Mullet , and Marie-Michèle Cordonnier-Pratt
Department of Plant Biology, University of Georgia, Athens, Georgia 30602
Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
Clemson University Genomics Institute, Clemson University, Clemson, South Carolina 29634
Department of Plant Pathology and Physiology, Clemson University, Clemson, South Carolina 29634
United States Department of Agriculture Agricultural Research Service, Southern Plains Agricultural Research Center, College Station, Texas 77845
Department of Plant and Soil Sciences, Texas Tech University, Lubbock, Texas 79409
Department of Statistics, University of Georgia, Athens, Georgia 30602
Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
* Corresponding author; email: lpratt{at}plantbio.uga.edu.
Improved knowledge of the sorghum transcriptome will enhance basic understanding of how plants respond to stresses and serve as a source of genes of value to agriculture. Toward this goal, Sorghum bicolor L. Moench cDNA libraries were prepared from light- and dark-grown seedlings, drought-stressed plants, Colletotrichum-infected seedlings and plants, ovaries, embryos, and immature panicles. Other libraries were prepared with meristems from Sorghum propinquum (Kunth) Hitchc. that had been photoperiodically induced to flower, and with rhizomes from S. propinquum and johnsongrass (Sorghum halepense L. Pers.). A total of 117,682 expressed sequence tags (ESTs) were obtained representing both 3' and 5' sequences from about half that number of cDNA clones. A total of 16,801 unique transcripts, representing tentative UniScripts (TUs), were identified from 55,783 3' ESTs. Of these TUs, 9,032 are represented by two or more ESTs. Collectively, these libraries were predicted to contain a total of approximately 31,000 TUs. Individual libraries, however, were predicted to contain no more than about 6,000 to 9,000, with the exception of light-grown seedlings, which yielded an estimate of close to 13,000. In addition, each library exhibits about the same level of complexity with respect to both the number of TUs preferentially expressed in that library and the frequency with which two or more ESTs is found in only that library. These results indicate that the sorghum genome is expressed in highly selective fashion in the individual organs and in response to the environmental conditions surveyed here. Close to 2,000 differentially expressed TUs were identified among the cDNA libraries examined, of which 775 were differentially expressed at a confidence level of 98%. From these 775 TUs, signature genes were identified defining drought, Colletotrichum infection, skotomorphogenesis (etiolation), ovary, immature panicle, and embryo.
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