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UD researchers report new work on rice genome
3:36 p.m., March 12, 2007--Important work in the deep sequencing of the genome for rice, an essential foodstuff for much of the world's population, is being reported by researchers at the University of Delaware and Ohio State University in the journal Nature Biotechnology. “This work represents a major advance in our understanding of the gene expression in what is arguably the world's most important crop plant, rice,” Blake C. Meyers, associate professor of plant and soil sciences who is affiliated with both UD's College of Agriculture and Natural Resources and the Delaware Biotechnology Institute, said. "Research on small RNAs is a leading edge in plant biotechnology," Machi Dilworth, director of the National Science Foundation's Division of Biological Infrastructure, said. "This work will contribute to an understanding of the role of small RNAs in gene expression not only in rice, but in all plants." In December 2004, the International Rice Genome Sequencing Project completed its work in what has been called a milestone of plant biology. Meyers said the UD and Ohio State researchers have “built on that resource by providing a unique, comprehensive and experimental assessment of rice transcription.” Using advanced sequencing technologies and high-powered computer-based informatics approaches, their work examined both normal gene expression (messenger ribonucleic acids, or mRNAs) as well as small ribonucleic acids (small RNAs) in rice. RNA is the only biological polymer that can both act as a catalyst, in the manner of proteins, and store key information, like deoxyribonucleic acid (DNA). The mRNAs encode proteins, while small RNAs, characterized by a length of just 20 to 25 nucleotides, play a vital role in regulating the plant's genes. Meyers said their analysis of rice was based on sequences representing nearly 47 million mRNA molecules and three million small RNAs, a substantially larger dataset than has been reported for any other plant species. Small RNAs are considered one of most important discoveries in biotechnology in the last 10 years. Because they are so much smaller than mRNAs, which are generally 500 to 5000 nucleotides, small RNAs went unnoticed for many years, or were considered biologically unimportant. Now they are known to play an important role in gene regulation, Meyers said, adding that deficiencies in small RNA production can have a profound effect on development, and small RNAs have been associated with other important biological processes, such as responses to stress. Determining the sequence of the small RNAs of an organism is critical for understanding their overall impact and individual biological roles, Meyers said, and the researchers have pioneered studies of small RNA by using several novel technologies to generate the data combined with computational approaches to analyze it. The technologies include Solexa Inc.'s transcriptional profiling technologies called Massively Parallel Signature Sequencing, or MPSS, and Sequencing-by-Synthesis, or SBS, as well as 454 Life Science's Inc.'s pyrosequencing-based method. All of these technologies are sequence-based analyses, so the data are highly specific with very low background, Meyers said. The Nature Biotechnology paper highlights their work with the MPSS technology. “The depth of both the mRNA and small RNA data is far greater than has been obtained for any plant species, including the model plant Arabidopsis, and our data suggest this depth of sampling is close to saturation,” Meyers said. These data are the first deep sequence data for small RNAs in a crop plant. “The rice small RNAs matched to five-fold more genomic locations than Arabidopsis, consistent with a greater genomic complexity and larger set of repeats,” Meyers said. “Many of the small RNAs will have related sequences in the many important cereal crop plants, including maize and wheat.” Among the mRNA data, Meyers said the researchers identified thousands of tissue-specific mRNA transcripts, including hundreds of specifically-expressed transposons, or potentially mobile DNA elements. With these data, the researchers developed a unique website to access this resource [http://mpss.udel.edu/rice]. The site will serve as starting point for gene expression analyses, map-based cloning and synteny studies for molecular biology work in many cereals. The website will also facilitate public access to these data. “In summary, our findings emphasize the power of the comprehensive analysis of mRNA and small RNAs, and our analyses provide an unparalleled examination of rice transcriptional complexity,” Meyers said. The work represents the combined efforts of three laboratories, two at UD and one at Ohio State. The UD laboratories, based at the Delaware Biotechnology Institute, are led by Meyers and by Pamela J. Green, Crawford H. Greenewalt Endowed Chair in Plant Molecular Biology. The Ohio State laboratory is led by Guo-Liang Wang, associate professor of plant pathology. Post-doctoral scientists Kan Nobuta, in the Meyers lab, and Cheng Lu, in the Green lab, as well as R.C. Venu, in the Wang lab, played key roles in the research and development of the publication. Additional assistance was provided by André Beló, a student in UD's Department of Plant and Soil Sciences, and Kalyan Vemaraju, Karthik Kulkarni, Wenzhong Wang and Manoj Pillay, all students in the Department of Computer and Information Sciences. The work is funded by the National Science Foundation and the U.S. Department of Agriculture. Article by Neil Thomas |
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