Abstract
Small RNAs play an important role in plant development, stress responses, and epigenetic regulation, primarily through their role in transcriptional and post-transcriptional silencing of specific target genes and loci. Most if not all plants utilize these small RNA signaling networks. We have developed a deep-sequencing based dataset of plant small RNAs, based on the hypothesis that comparisons among the complex pool of small RNAs from diverse plants will identify novel types of conserved, regulated, or species-specific molecules. A database containing upward of hundreds of millions of plant small RNA sequences is being created for comparative analyses. This small RNA database will allow the experimental characterization of the majority of the biologically important small RNAs for a range of plant species. This database can be accessed from our website (http://smallrna.udel.edu/). A variety of web-based tools have been developed for analyses of these data. Here, we focus on these tools, and we describe how the users can implement these tools to analyze and interpret the small RNA data and how the users could use similar approaches for other sets of plant small RNAs from diverse species.
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Acknowledgments
We are grateful to Prakash Janardhan, Mayumi Nakano, Vimal Kannan, Emanuele De Paoli, Pam Green, and other members of the Meyers and Green labs for assistance with the database, web pages, analytical tools, data and discussions about all of these. Work on this project is supported by the NSF Plant Genome Research Program, Comparative Sequencing Project, award #0638525.
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Mahalingam, G., Meyers, B.C. (2010). Computational Methods for Comparative Analysis of Plant Small RNAs. In: Meyers, B., Green, P. (eds) Plant MicroRNAs. Methods in Molecular Biology, vol 592. Humana Press. https://doi.org/10.1007/978-1-60327-005-2_12
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DOI: https://doi.org/10.1007/978-1-60327-005-2_12
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